Protist classification

A protist is any eukaryotic organism that is not an animal, plant, or fungus. The protists do not form a natural group, or clade, since they exclude certain eukaryotes with whom they share a common ancestor; but, like algae or invertebrates, the grouping is used for convenience. In some systems of biological classification, such as the popular five-kingdom scheme proposed by Robert Whittaker in 1969, the protists make up a kingdom called Protista, composed of "organisms which are unicellular or unicellular-colonial and which form no tissues". In the 21st century, the classification shifted toward a two-kingdom system of protists: Chromista and Protozoa.
The following groups contain protists. The clade Opisthokonta also contains the animals and the fungi, and the kingdom Archaeplastida also contains algae and plants.
Legend:

Amorphea

The supergroup Amorphea contains very diverse heterotrophic organisms, from the macroscopic fungi and animals to the unicellular choanoflagellates and classical amoebae. They frequently exhibit the ability to produce multinucleated cells, a trait considered ancestral to Amorphea. They are also capable of producing pseudopodia, as does the closely related CRuMs clade, forming the clade Podiata.
Amorphea is divided into two clades: Amoebozoa, containing well-known amoebae and slime molds, and Obazoa, containing animals, fungi, and their closest relatives. The relationship between these two clades was initially called 'Unikonta', due to a hypothesis where their common ancestor was a unikont, i.e., a eukaryote with just one flagellum. However, this hypothesis was refuted, as there are bikont amorpheans and it likely is not an ancestral trait to have a single flagellum.

Obazoa

The clade Obazoa contains two small groups of flagellates, the breviates and the apusomonads, and
the large clade Opisthokonta, which contains animals, fungi, and their closest protist relatives. Under the Cavalier-Smith system, breviates and apusomonads were two classes that composed the phylum Apusozoa, but this taxon is paraphyletic, as apusomonads are more closely related to opisthokonts. The taxonomy of apusomonads was expanded in a 2022 phylogenetic study that introduced many new genera.

Class Breviatea, order Breviatida, family Breviatidae, genera Breviata, Lenisia, Pygsuia, Subulatomonas.
Class Thecomonadea, order Apusomonadida, family Apusomonadidae. Genera not assigned to any subfamily: Amastigomonas, Multimonas, Podomonas, Catacumbia, Cavaliersmithia.
*Subfamily Apusomonadinae, genera Apusomonas, Manchomonas.
*Subfamily Thecamonadinae, genera Chelonemonas, Karpovia, Singekia, Thecamonas.

Opisthokonta

Opisthokonts are divided into two branches: Holozoa, containing the ichthyosporeans, pluriformeans, filastereans and choanoflagellates; and Nucletmycea or Holomycota, containing the nucleariids and opisthosporidians. These groups, minus opisthosporidians, were classified as different classes within the paraphyletic phylum Choanozoa in the system of Cavalier-Smith, now obsolete. Instead, Choanozoa is the name used for the clade containing choanoflagellates and animals. opisthosporidians are often studied as protists, but are also considered fungi by protistologists and mycologists alike. Both Holozoa and Nucletmycea have been proposed once as superkingdoms by a group of mycologists who classified nucleariids and fungi as kingdoms, but without any mention of holozoan kingdoms.

Nucletmycea
*Order Rotosphaerida, family Nucleariidae, genera: Fonticula, Nuclearia, Parvularia, Pompholyxophrys, Lithocolla, Vampyrellidium, Elaeorhanis, Pinaciophora, Rabdiophrys, Rabdiaster, Thomseniophora.
*Kingdom Fungi
Holozoa. Genera incertae sedis: Tunicaraptor, Bicellum.
*Class Ichthyosporea
**Order Dermocystida, family Rhinosporidaceae, genera Amphibiocystidium, Amphibiothecum, Chromosphaera, Dermocystidium, Rhinosporidium, Sphaerothecum, Valentines.
**Order Ichthyophonida, family Amoebidiidae, genera Abeoforma, Amoebidium, Anurofeca, Astreptonema, Caullerya, Creolimax, Eccrinidus, Enterobryus, Enteropogon, Ichthyophonus, Palavascia, Pseudoperkinsus, Psorospermium, Sphaeroforma.
*Class Pluriformea, order Corallochytrida
**Family Corallochytriidae, genus Corallochytrium.
**Family Syssomonadidae, genus Syssomonas.
*Class Filasterea, order Ministeriida. Genus not assigned to any family: Pigoraptor.
**Family Ministeriidae, genus Ministeria.
**Family Capsasporidae, genus Capsaspora.
**Family Txikisporidae, genus Txikispora.
*Choanozoa
**Class Choanoflagellata
***Order Craspedida, family Salpingoecidae, genera Astrosiga, Aulomonas, Barroeca, Choanoeca, Cladospongia, Codonocladium, Codonosigopsis, Codosiga, Desmarella, Dicraspedella, Diploeca, Diplosiga, Diplosigopsis, Hartaetosiga, Kentia, Lagenoeca, Microstomoeca, Monosiga, Mylnosiga, Pachysoeca, Proterospongia, Salpingoeca, Salpingorhiza, Sphaeroeca, Stagondoeca, Stelexomonas, Stylochromonas.
***Order Acanthoecida
****Family Acanthoecidae, genera Acanthoeca, Enibas, Helgoeca, Polyoeca, Savillea.
****Family Stephanoecidae, genera Acanthocorbis, Amoenoscopa, Apheloecion, Bicosta, Calliacantha, Calotheca, Campanoeca, Campyloacantha, Conion, Cosmoeca, Crinolina, Crucispina, Diaphanoeca, Didymoeca, Kakoeca, Monocosta, Nannoeca, Parvicorbicula, Thomsenella, Pleurasiga, Polyfibula, Saepicula, Saroeca, Spinoeca, Spiraloecion, Stephanacantha, Stephanoeca, Syndetophyllum.
**Kingdom '''Metazoa'''

Amoebozoa

The phylum Amoebozoa contains around 2,400 species of primarily amoeboid protists. It includes a large portion of the traditional Sarcodina, the taxon uniting all amoebae. In particular, it groups naked and testate lobose amoebae, as well as the archamoebae and eumycetozoans, and a few flagellates. After the general 2019 revisions published by the International Society of Protistologists, there have been specific revisions to the classification of eumycetozoans and testate amoebae.
Phylum Amoebozoa. Genera incertae sedis: Belonocystis, Boveella, Biomyxa, Corallomyxa, Gibbodiscus, Hartmannia, Malamoeba, Malpighamoeba, Oscillosignum, Pseudothecamoeba, Rhabdamoeba, Schoutedamoeba, Stereomyxa, Subulamoeba, Triaenamoeba, Unda.

Class Tubulinea
*Corycidia
**Order Trichosida, family Trichosphaeriidae, genus Trichosphaerium.
**Family Microcoryciidae, genera Amphizonella, Diplochlamys, Microcorycia*, Parmulina*, Penardochlamys*, Zonomyxa*.
*Order Echinamoebida
**Family Echinamoebidae, genera Echinamoeba, Micriamoeba.
**Family Vermamoebidae, genus Vermamoeba.
*Elardia
**Order Leptomyxida
***Family Leptomyxidae, genus Leptomyxa.
***Family Rhizamoebidae, genus Rhizamoeba.
***Family Flabellulidae, genus Flabellula.
***Family Gephyramoebidae, genus Gephyramoeba.
**Superorder Eulobosia
***Order Euamoebida
****Family Amoebidae, genera: Amoeba, Chaos, Polychaos, Parachaos, Trichamoeba, Deuteramoeba, Hydramoeba.
****Family Hartmannellidae, genera Cashia, Copromyxa, Copromyxella, Glaeseria, Hartmannella, Ptolemeba, Saccamoeba.
****Family Nolandellidae, genus Nolandella.
***Order Arcellinida. Genera incertae sedis: Acipyxis, Apolimia, Argynnia, Armipyxis, Conicocassis, Cornuapyxis, Ellipsopyxella, Ellipsopyxis, Erugomicula, Frenopyxis, Geamphorella, Geoplagiopyxis, Geopyxella, Hoogenraadia, Jungia, Lagenodifflugia, Lamptopyxis, Lamtoquadrula, Leptochlamys, Maghrebia, Meisterfeldia, Microquadrula, Nabranella, Oopyxis, Paracentropyxis, Paraquadrula, Pentagonia, Physochila, Planhoogenraadia, Pomoriella, Pontigulasia, Prantlitina, Proplagiopyxis, Protoplagiopyxis, Protocucurbitella, Pseudawerintzewia, Pseudonebela, Schoenbornia, Sexangularia, Suiadifflugia, Trigonopyxis, Wailesella, Cangwuella.
****Suborder Phryganellina
*****Family Phryganellidae, genus Phryganella.
*****Family Cryptodifflugiidae, genus Cryptodifflugia.
****Suborder Organoconcha, family Microchlamyiidae, genera Microchlamys, Spumochlamys, Pyxidicula.
****Suborder Glutinoconcha
*****Infraorder Volnustoma, family Heleoperidae, genera Heleopera, Metaheleopera.
*****Infraorder Hyalospheniformes, family Hyalospheniidae, genera Alabasta, Alocodera, Apodera, Certesella, Cornutheca, Gibbocarina, Hyalosphenia, Longinebela, Mrabella, Nebela, Padaungiella, Planocarina, Porosia, Quadrulella.
*****Infraorder Excentrostoma, family Centropyxidae, genera Awerinzewia, Bullinularia, Centropyxis, Frenopyxis, Golemanskia, Plagiopyxis.
*****Infraorder Cylindrothecina, family Cylindrifflugiidae, genus Cylindrifflugia.
*****Infraorder Longithecina
******Family Difflugiidae, genera Difflugia, Zivkovicia.
******Family Lesquereusiidae, genus Lesquereusia.
*****Infraorder Sphaerothecina
******Family Arcellidae, genera Arcella, Galeripora.
******Family Netzeliidae, genera Cucurbitella, Cyclopyxis, Netzelia.
Class Discosea
*Subclass Flabellinia
**Superorder Dermelia
***Order Mycamoebida, family Mycamoebidae, genera Mycamoeba, Janelia, Microglomus.
***Order Dermamoebida
****Family Dermamoebidae, genera Dermamoeba, Paradermamoeba, Coronamoeba.
****Family Mayorellidae, genus Mayorella.
**Superorder Thecavania
***Order Stygamoebida, family Stygamoebidae, genera Stygamoeba, Vermistella.
***Order Thecamoebida, genera Sappinia, Stenamoeba, Stratorugosa, Thecamoeba, Thecochaos.
***Order Dactylopodida, genera Cunea, Janickina, Korotnevella, Neoparamoeba, Paramoeba, Pseudoparamoeba, Vexillifera.
***Order Vannellida, family Vannellidae, genera Clydonella, Lingulamoeba, Paravannella, Pessonella, Ripella, Vannella.
*Subclass Centramoebia
**Order Acanthopodida, genera Acanthamoeba, Balamuthia, Luapeleamoeba, Protacanthamoeba, Dracoamoeba, Vacuolamoeba.
**Order Himatismenida, genera Cochliopodium, Ovalopodium, Parvamoeba.
**Order Pellitida, genera Endostelium, Gocevia, Paragocevia, Pellita.
Evosea
*Class Cutosea, order Squamocutida
**Family Squamamoebidae, genera Armaparvus, Squamamoeba.
**Family Sapocribridae, genus Sapocribrum.
**Family Idionectidae, genus Idionectes.
*Class Variosea. Genera not assigned to any lower clade: Angulamoeba, Arboramoeba, Darbyshirella, Dictyamoeba, Ischnamoeba, Heliamoeba, Filamoeba, Phalansterium.
**Family Flamellidae, genera Flamella, Telaepolella.
**Order Protosteliida, family Protosteliidae, genus Protostelium.
**Order Fractovitellida
***Family Acramoebidae, genus Acramoeba.
***Family Schizoplasmodiidae, genera Ceratiomyxella, Nematostelium, Schizoplasmodium.
***Family Soliformoviidae. Genera: Soliformovum ; Grellamoeba.
**Order Cavosteliida, family Cavosteliidae, genera Cavostelium, Schizoplasmodiopsis, Tychosporium.
**Order Holomastigida, family Multiciliidae, genera Artodiscus, Multicilia.
*Class Archamoebea
**Family Tricholimacidae, genus Tricholimax.
**Order Entamoebida, family Entamoebidae, genera Entamoeba, Entamoebites.
**Order Pelobiontida
***Suborder Pelomyxina, family Pelomyxidae, genera Mastigella, Pelomyxa.
***Suborder Mastigamoebina
****Family Rhizomastixidae, genus Rhizomastix.
****Family Mastigamoebidae, genera Endamoeba*, Endolimax, Iodamoeba, Mastigamoeba, Mastigina*.
*Eumycetozoa
**Class Dictyostelea . Genus unassigned to any order: Synstelium. Genus incertae sedis: Coenonia.
***Order Acytosteliales
****Family Acytosteliaceae, genera Acytostelium, Rostrostelium, Heterostelium.
****Family Cavenderiaceae, genus Cavenderia.
***Order Dictyosteliales. Genus unassigned to any family: Coremiostelium.
****Family Dictyosteliaceae, genera Dictyostelium, Polysphondylium.
****Family Raperosteliaceae, genera Hagiwaraea, Raperostelium, Speleostelium, Tieghemostelium.
**Class Ceratiomyxomycetes, order Protosporangiida
***Family Ceratiomyxaceae, genus Ceratiomyxa.
***Family Protosporangiidae, genera Clastostelium, Protosporangium.
**Class Myxogastrea
***Subclass Lucisporinia . Genera incertae sedis: Arcyriatella, Calonema, Minakatella, Trichioides.
****Superorder Cribariidia, order Cribariales, family Cribariaceae, genera Cribaria, Lindbladia, Licaethalium.
****Superorder Trichiidia
*****Order Reticulariales, family Reticulariaceae, genera: Alwisia, Lycogala, Reticularia, Tubifera.
*****Order Liceales, family Liceaceae, genera Licea, Listerella.
*****Order Trichiales
******Family Dianemataceae, genera Calomyxa, Dianema, Dictydiaethalium, Prototrichia.
******Family Trichiaceae, genera Hemitrichia, Arcyria ; Perichaena, Trichia.
***Subclass Columellinia . Genera incertae sedis: Diachea, Echinosteliopsis, Leptoderma, Paradiachea, Protophysarum, Trabrooksia, Willkommlangea.
****Superorder Echinosteliidia, order Echinosteliales, family Echinosteliaceae, genera: Barbeyella, Echinostelium.
****Superorder Stemonitidia
*****Order Clastodermatales, family Clastodermataceae, genus Clastoderma.
*****Order Meridermatales, family Meridermataceae, genus Meriderma.
*****Order Stemonitales
******Family Stemonitidaceae, genera Macbrideola, Stemonitis, Symphytocarpus.
******Family Amaurochaetaceae, genera Comatricha, Stemonaria, Stemonitopsis, Amaurochaete, Brefeldia, Enerthenema, Paradiacheopsis.
*****Order Physarales . Genus not assigned to any family: Tasmaniomyxa.
******Family Lamprodermataceae, genera Lamproderma, Collaria.
******Family Didymiaceae, genera Diderma, Didymium, Lepidoderma, Mucilago.
******Family Physaraceae, genera Craterium, Leocarpus, Fuligo, Physarum, Physarella, Physarina, Kelleromyxa.

Archaeplastida

Division Glaucophyta . Incertae sedis genera: Archaeopsis, Chalarodora, Glaucocystopsis, Peliaina, Strobilomonas.
*Order Cyanophorales. Sole genus: Cyanophora.
*Order Glaucocystales. Sole genus: Glaucocystis.
*Order Gloeochaetales. Genera: Cyanoptyche, Gloeochaete.
Phylum Picozoa → class Picomonadea → order Picomonadida → family Picomonadidae. Sole genus: Picomonas.
Phylum Rhodelphidia → class Rhodelphidea → order Rhodelphida → family Rhodelphidae. Sole genus: Rhodelphis.
Division '''Rhodophyta'''

Chloroplastida

Division Prasinodermophyta
*Class Prasinodermophyceae → order Prasinodermatales → family Prasinodermataceae. Sole genus: Prasinoderma.
*Class Palmophyllophyceae
**Order Palmophyllales → family Palmophyllaceae. Genera: Palmophyllum ; Verdigellas ; Palmoclathrus.
**Order Prasinococcales → family Prasinococcaceae. Sole genus: Prasinococcus.
Division Chlorophyta
*Class Chloropicophyceae → order Chloropicales → family Chloropicaceae. Genera: Chloroparvula ; Chloropicon.
*Class Mamiellophyceae
**Order Mamiellales
***Family Bathycoccaceae. Genera: Bathycoccus ; Ostreococcus.
***Family Mamiellaceae. Genera: Mamiella ; Mantoniella ; Micromonas.
**Order Dolichomastigales
***Family Crustomastigaceae. Sole genus: Crustomastix.
***Family Dolichomastigaceae. Sole genus: Dolichomastix.
**Order Monomastigales → family Monomastigaceae. Sole genus: Monomastix.
*Class Nephroselmidophyceae → order Nephroselmidales → family Nephroselmidaceae. Genera: Nephroselmis.
*Class Picocystophyceae → order Picocystales → family Picocystaceae. Sole genus: Picocystis.
*Class Pseudoscourfieldiophyceae → order Pseudoscourfieldiales → family Pseudoscourfieldiaceae .
*Class Pyramimonadophyceae → order Pyramimonadales
**Family Pyramimonadaceae. Genera: Cymbomonas ; Pyramimonas ; "Prasinopapilla".
**Family Halosphaeraceae. Genera: Halosphaera ; Pachysphaera ; Tasmanites.
*Core Chlorophyta
**Class Chlorodendrophyceae → order Chlorodendrales → family Chlorodendraceae. Genera: Prasinocladus ; Scherffelia ; Tetraselmis.
**Class Pedinophyceae
***Order Marsupiomonadales
****Family Marsupiomonadaceae. Sole genus: Marsupiomonas.
****Family Resultomonadaceae. Sole genus: Resultomonas.
***Order Pedinomonadales → family Pedinomonadaceae. Genera: Chlorochytridion ; Pedinomonas.
**UTC clade
***Class Chlorophyceae
****SV clade
*****Order Sphaeropleales. Incertae sedis genera: Spermatozopsis ; Golenkinia ; Jenufa ; Johansenicoccus.
******Family Dictyochloridaceae. Sole genus: Dictyochloris.
******Family Sphaeropleaceae
******Family Microsporaceae
******Treubarinia. Genera: Trochiscia ; Treubaria ; Cylindrocapsa ; Elakatothrix.
******Scenedesminia
*******Family Bracteacoccaceae. Sole genus: Bracteacoccus.
*******Family Bracteamorphaceae. Sole genus: Bracteamorpha.
*******Family Chromochloridaceae. Sole genus: Chromochloris.
*******Family Dictyococcaceae. Sole genus: Dictyococcus.
*******Family Hydrodictyaceae. Genera: Hydrodictyon ; Lacunastrum ; Monactinus ; Parapediastrum ; Pediastrum.
*******Family Mychonastaceae. Sole genus: Mychonastes.
*******Family Neochloridaceae
*******Family Pseudomuriellaceae. Sole genus: Pseudomuriella.
*******Family Scenedesmaceae
*******Family Schizochlamydaceae. Sole genus: Schizochlamys.
*******Family Selenastraceae
*******Family Radiococcaceae
*******Family Rotundellaceae. Sole genus: Rotundella.
*******Family Tumidellaceae. Sole genus: Tumidella.
*****Order Volvocales
****OCC clade
*****Order Chaetopeltidales
*****Order Chaetophorales
*****Order Oedogoniales
***Class Trebouxiophyceae
***Class Ulvophyceae
Division Streptophyta
*Class Chlorokybophyceae → order Chlorokybales → family Chlorokybaceae. Sole genus: Chlorokybus.
*Class Mesostigmatophyceae → order Mesostigmales → family Mesostigmataceae. Sole genus: Mesostigma.
*Class Klebsormidiophyceae
**Order Klebsormidiales → family Klebsormidiaceae. Genera: Klebsormidium ; Interfilum ; Streptofilum.
**Order Entransiales → family Entransiaceae. Sole genus: Entransia.
**Order Hormidiellales → family Hormidiellaceae. Genera: Hormidiella ; Streptosarcina.
*Phragmoplastophyta
**Class Charophyceae
**Class Coleochaetophyceae
**Anydrophyta
***Class Zygnematophyceae
****Order Serritaeniales → family Serritaeniaceae. Sole genus: Serritaenia.
****Order Zygnematales → family Zygnemataceae. Genera: Cylindrocystis ; Mesotaenium ; Mougeotia ; Zygnema ; Zygnemopsis.
****Order Desmidiales → family Desmidiaceae. Genera: Bambusina ; Closterium ; Cosmarium ; Cosmocladium ; Desmidium ; Euastrum ; Micrasterias ; Netrium ; Nucleotaenium ; Onychonema ; Penium ; Phymatodocis ; Planotaenium ; Pleurotaenium ; Staurastrum ; Staurodesmus ; Xanthidium ; etc.
****Order Spirogyrales. Sole genus: Spirogyra
***Embryophyta . Excluded from protists.

Pancryptista

The phylum Cryptista contains heterotrophic and photosynthetic single-celled flagellates. Its classification has undergone many changes through the years, and several conflicting systems and nomenclatures coexist. It was described by Thomas Cavalier-Smith in 1989 to unite two distinct groups of flagellates: the photosynthetic cryptomonads, and the heterotrophic goniomonads. The name Cryptista was meant to be a synonym of Cryptophyta, the algal division described by the same author in previous years. In 2004, he modified the classification of Cryptista to add two subphyla: Cryptomonada, containing the aforementioned classes, and Leucocrypta, containing the heterotrophic katablepharids. The next year, a separate group of authors proposed a different higher ranking for katablepharids as a phylum Kathablepharida or division Katablepharidophyta, related to but independent from phylum Cryptophyta, with no mention of Cryptista. Between 2013 and 2015, Cavalier-Smith updated the classification once more by describing three new subphyla: Rollomonadia, containing the previous subphyla lowered to superclasses; Palpitia, containing the flagellate Palpitomonas bilix; and Corbihelia, containing picozoans, telonemids, and some heliozoan species. Corbihelia did not reach consensus: later analyses and revisions separated telonemids and picozoans as their own clades, and placed Heliomorpha in Cercozoa. However, the addition of Palpitomonas and the monophyly of Rollomonadia have been supported in other analyses.
Cryptista was redefined in the 2019 ISOP revision as the clade containing Palpitomonas, katablepharids, goniomonads and cryptomonads. However, this revision introduced yet another classification system that is contradictory with the previous ones. They proposed a single class Cryptophyceae uniting cryptomonads, goniomonads and katablepharids, and treated cryptomonads as a single order Cryptomonadales, although this does not follow scientific consensus: there are more cryptomonad orders and the name Cryptophyceae was already used for taxa that excluded katablepharids and often excluded goniomonads too. There has not been a new revision since.
Unlike with Heliomorpha, the genus Microheliella was genetically sequenced and its affinities have been resolved. In 2022, it was proposed as the sister group of Cryptista, in a clade known as Pancryptista.
Pancryptista

Order Microhelida, family Microheliellidae, genus Microheliella.
Phylum Cryptista
*Subphylum Palpitia, class Palpitea, order Palpitida, family Palpitomonadidae, genus Palpitomonas.
*Subphylum Rollomonadia
**Superclass Leucocrypta, class Leucocryptea, order Kathablepharidida, family Kathablepharididae, genera Hatena, Kathablepharis, Leucocryptos, Platychilomonas, Roombia.
**Superclass Cryptomonada
***Class Goniomonadea
****Order Goniomonadida, family Goniomonadidae, genera Aquagoniomonas, Baltigoniomonas, Cosmogoniomonas, Goniomonas, Limnogoniomonas, Marigoniomonas, Neptunogoniomonas, Poseidogoniomonas, Thalassogoniomonas.
****Order Hemiarmida, family Hemiarmidae, genus Hemiarma.
***Class Cryptophyceae . Genera incertae sedis: Bjornbergiella, Cyanomonas, Plagioselmis.
****Order Cryptomonadales
*****Family Baffinellaceae, genus Baffinella.
*****Family Cryptomonadaceae, genera Cryptomonas, Chilomonas.
****Order Pyrenomonadales
*****Family Pyrenomonadaceae, genera Pyrenomonas, Storeatula, Rhinomonas.
*****Family Geminigeraceae, genera Geminigera, Teleaulax, Hanusia, Guillardia, Proteomonas.
*****Family Chroomonadaceae, genera Chroomonas, Falcomonas, Komma.
*****Family Hemiselmidaceae, genus Hemiselmis.
****Order Tetragonidiales, family Tetragonidiaceae, genus Tetragonidium.

Haptista

Haptophyta
*Pavlovales . Diacronema, Exanthemachrysis, Pavlova, Rebecca.
*Prymnesiophyceae
**Prymnesiales. Chrysochromulina, Chrysocampanula, Dicrateria, Haptolina, Prymnesium, Pseudohaptolina.
**Phaeocystales. Phaeocystis.
**Isochrysidales. Emiliania, Gephyrocapsa, Isochrysis, Ruttnera, Tisochrysis.
**Coccolithales. Balaniger, Calciosolenia, Coccolithus, Hymenomonas, Chrysotila, Wigwamma.
*Rappephyceae
**Pavlomulinales. Pavlomulina.
Class Centroplasthelida . Genera incertae sedis: Meringosphaera, Parasphaerastrum.
*Family Spiculophryidae, genus Spiculophrys.
*Superorder Pterocystida
**Order Raphidista
***Family Choanocystidae, genus Choanocystis.
***Family Raphidiophryidae, genus Raphidiophrys.
**Order Pterista
***Family Oxnerellidae, genus Oxnerella.
***Family Pterocystidae, genera Pterocystis, Raineriophrys, Chlamydaster, Pseudoraphidiophrys, Pseudoraphidocystis, Triangulopteris, Khitsovia.
***Family Heterophryidae, genera Heterophrys, Sphaerastrum.
***Family Clypiferidae, genus Clypifer.
*Superorder Panacanthocystida
**Order Chthonida, suborder Yogsothothina, family Yogsothothidae, genera Yogsothoth, Pinjata.
**Order Acanthocystida
***Suborder Marophryina, family Marophryidae, genus Marophrys.
***Suborder Chalarothoracina
****Family Acanthocystidae, genus Acanthocystis.
****Family Raphidocystidae, genus Raphidocystis.

Stramenopiles

Class Platysulcea → order Platysulcida → family Platysulcidae. Sole genus: Platysulcus.
Family Kaonashiidae. Sole genus: Kaonashia.

Bigyra

Subphylum Opalozoa
*Infraphylum Placidozoa
**Class Placididea → order Placidida → family Placididae. Genera: Allegra ; Haloplacidia ; Pendulomonas ; Placidia ; Placilonga ; Suigetsumonas ; Wobblia.
**Class Nanomonadea → order Uniciliatida
***Family Incisomonadidae. Sole genus: Incisomonas.
***Family Solenicolidae. Sole genus: Solenicola.
**Class Opalomonadea . No described species.
**Superclass Opalinata
***Class Opalinea
****Order Proteromonadida → family Proteromonadidae. Sole genus: Proteromonas .
****Order Opalinida
*****Family Karotomorphidae. Sole genus: Karotomorpha.
*****Family Opalinidae. Genera: Cepedea ; Opalina ; Protoopalina ; Protozelleriella ; Zelleriella.
***Class Blastocystea → order Blastocystida → family Blastocystidae. Sole genus: Blastocystis.
*Infraphylum Bikosea → class Bikosea. Genera not assigned to families: Bilabrum ; Cafileria ; Cantina.
**Family Pseudobodonidae. Sole genus: Pseudobodo.
**Subclass Rictidia → order Rictida → family Rictidae. Sole genus: Rictus.
**Subclass Bicosidia/Bicosoecophycidae
***Superorder Borokiae → order Borokida/Borokales → family Borokidae/Borokaceae. Sole genus: Boroka.
***Superorder Cyathobodoniae. Incertae sedis genus: Halocafeteria.
****Order Anoecida/Anoecales
*****Family Anoecidae/Anoecaceae. Sole genus: Anoeca.
*****Family Caecitellidae/Caecitellaceae. Sole genus: Caecitellus.
*****Family Cafeteriidae/Cafeteriaceae. Sole genus: Cafeteria.
*****Family Symbiomonadaceae. Sole genus: Symbiomonas.
****Order Bicoecida/Bicoecales
*****Family Bicosoecidae. Genera: Bicosoeca ; Stephanocodon ; Poteriodendron.
*****Family Labromonadidae. Sole genus: Labromonas.
****Order Pseudodendromonadida/Pseudodendromonadales.
*****Family Pseudodendromonadidae/Pseudodendromonadaceae. Genera: Cyathobodo ; Pseudodendromonas.
*****Family Siluaniidae/Siluaniaceae. Genera: Adriamonas ; Siluania ; Otto ; Regin.
*****Family Paramonadidae/Paramonadaceae. Sole genus: Paramonas.
*****Family Nanidae/Nanaceae. Sole genus: Nanum.
*****Family Neradidae/Neradaceae. Sole genus: Nerada.
*****Family Filidae/Filaceae. Sole genus: Filos.
Subphylum Sagenista
*Class Labyrinthulomycetes
**Order Amphitremida
***Family Amphitremidae. Genera: Amphitrema; Archerella; Paramphitrema.
***Family Diplophryidae. Sole genus: Diplophrys.
**Order Amphifilida
***Family Amphifilidae. Sole genus: Amphifila.
***Family Sorodiplophryidae. Genera: Fibrophrys ; Sorodiplophrys.
**Order Oblongichytrida/Oblongichytriales → family Oblongichytriidae/Oblongichytriaceae. Sole genus: Oblongichytrium.
**Order Labyrinthulida /Labyrinthulales
***Family Aplanochytriidae/Aplanochytriaceae. Sole genus: Aplanochytrium .
***Family Labyrinthulidae /Labyrinthulaceae. Sole genus: Labyrinthula .
***Family-level clade "Stellarchytriidae/Stellarchytriaceae". Sole genus: Stellarchytrium.
**Order Thraustochytrida/Thraustochytriales
***Family Althorniidae/Althornidiaceae. Sole genus: Althornia.
***Family Thraustochytriidae/Thraustochytriaceae. Genera: Aurantiochytrium ; Botryochytrium ; Japonochytrium ; Monorhizochytrium ; Parietichytrium ; Phycophthorum ; Schizochytrium ; Sicyoidochytrium ; Thraustochytrium ; Ulkenia.
*Class Eogyrea . Genera not assigned to families: Mastreximonas ; Vomastromonas.
**Order Eogyrida → family Pseudophyllomitidae/Pseudophyllomitaceae. Sole genus: Pseudophyllomitus.

Gyrista

Subphylum Bigyromonada
*Class Developea → order Developayellida /Developayellales → family Developayellidae/Developayellaceae. Genera: Cubaremonas ; Develocanicus ; Develocauda ; Developayella ; Develorapax ; Mediocremonas.
*Class Pirsonea → order Pirsoniales → Pirsoniaceae. Genera: Bordeauxia ; Bullionia ; Feodosia ; Koktebelia ; Noirmoutieria ; Pirsonia.
Subphylum Pseudofungi
*Class Hyphochytrea /Hyphochytriomycetes → order Hyphochytriales
**Family Anisolpidiaceae. Genera: Anisolpidium ; Canteriomyces.
**Family Hyphochytridiomycetaceae. Sole genus: Hyphochytrium.
**Family Rhizidiomycetaceae. Latrostium ; Rhizidiomyces ; Rhizidiomycopsis.
*Class Oomycetes . Incertae sedis genera: Atkinsiella ; Ciliatomyces ; Crypticola ; Ectrogella ; Eurychasma ; Halodaphnea ; Haliphthoros ; Haptoglossa ; Lagena ; Lagenisma ; Olpidiopsis ; Pontisma ; Pythiella ; Rozellopsis ; Sirolpidium.
**Saprolegnialean lineage. Achlya ; Aphanomyces ; Aplanopsis ; Apodachlya ; Aquastella ; Geolegnia ; Leptomitus ; Newbya ; Pythiopsis ; Protoachlya ; Salisapilia ; Saprolegnia ; Thraustotheca.
**Peronosporalean lineage. Albugo ; Bremia ; Chlamydomyzium ; Halophytopthora ; Hyaloperonospora ; Lagenidium ; Myzocytiopsis ; Peronospora ; Plasmopara ; Pythium ; Pseudoperonospora ; Phytophthora ; Phytopythium ; Pustula.
Subphylum/Division Ochrophytina/'Ochrophyta' . Incertae sedis genera: Commation.
*Order Actinophryida
**Suborder Actinosphaerina → family Actinosphaeriidae. Sole genus: Actinosphaerium .
**Suborder Actinophryina
***Family Actinophryidae. Sole genus: Actinophrys .
***Family Helioraphidae. Sole genus: Heliorapha.
*Infraphylum Chrysista. Incertae sedis genera: Chrysoderma ; Chrysomeris ; Chrysonephos ; "Giraudyopsis" ; Rhamnochrysis.
**Class Eustigmatophyceae
***Clade Goniochloridales. Genera: Goniochloris ; Pseudostaurastrum ; Tetraedriella ; Trachydiscus ; Trebonskia ; Vacuoliviride.
***Order Eustigmatales
****Paraeustigmatos
****Family Eustigmataceae. Genera: Ellipsoidion ; Chlorobotrys ; Eustigmatos ; Pseudocharaciopsis ; Vischeria.
****Family Monodopsidaceae . Genera: Microchloropsis ; Monodopsis ; Nannochloropsis ; Pseudotetraedriella.
****Family Neomonodaceae. Genera: Botryochloropsis ; Characiopsella ; Munda ; Neomonodus ; Pseudellipsoidion.
**SII clade
***Class Olisthodiscophyceae → order Olisthodiscales → family Olisthodiscaceae. Sole genus: Olisthodiscus.
***Class Pinguiophyceae → order Pinguiochrysidales → family Pinguiochrysidaceae. Genera: Glossomastix ; Phaeomonas ; Pinguiochrysis ; Pinguiococcus ; Polypodochrysis.
***SSC clade
****Chrysophyceae. Incertae sedis taxa: Chryososaccus, Chrysosphera, Cyclonexis, Lygynion, Phaeoplaca.
*****Chromulinales. Chromulina, Chrysomonas.
*****Hibberdiales. Hibberdia.
*****Ochromonadales. Spumella, Pedospumella, Ochromonas.
*****Paraphysomonadida. Paraphysomonas.
*****Synurales. Chrysodidymus, Mallomonas, Synura, Tesselaria.
****Picophagea . Chlamydomyxa, Chrysopodocystis, Guanochroma, Leukarachnion, Picophagus, Synchroma.
**SI clade/PXR clade
***Class Raphidophyceae → order Chattonellales . Genera: Chattonella, Fibrocapsa, Goniostomum, Haramonas, Heterosigma, Merotricha, Vacuolaria.
***PX clade
****Class Chrysoparadoxophyceae → order Chrysoparadoxales → family Chrysoparadoxaceae. Genera: Chrysoparadoxa ; Nematochrysis .
****Phaeophyceae
*****Ascoseirales. Ascoseira.
*****Desmarestiales. Arthrocladia, Desmarestia, Himantothallus, Phaeurus.
*****Dictyotales. Dictyota, Dilophus, Lobophora, Padina, Stypopodium, Taonia, Zonaria.
*****Discosporangiales. Choristocarpus, Discosporangium.
*****Ectocarpales. Adenocystis, Acinetospora, Asterocladon, Asteronema, Chordaria, Ectocarpus, Scytosiphon.
*****Fucales. Ascophyllum, Bifurcaria, Cystoseira, Druvillaea, Fucus, Hormosira, Sargassum, Turbinaria.
*****Ishigeales . Ishige.
*****Laminariales. Akkesiophycus, Alaria, Chorda, Costaria, Laminaria, Lessonia, Pseudochoda.
*****Nemodermatales. Nemoderma.
*****Onslowiales. Onslowia.
*****Ralfsiales. Lithoderma, Neoralfsia, Pseudolithoderma, Ralfsia.
*****Scytothamnales. Scytothamnus, Splachnidium, Stereocladon.
*****Sphacelariales. Chaetopteris, Halopteris, Stypocaulon, Sphacelaria, Verosphacella.
*****Sporochnales. Bellotia, Carpomitra, Nereia, Sporochonus, Tomaculopsis.
*****Syringodermatales. Syringoderma.
*****Tilopteridales. Cutleria, Halosiphon, Haplospora, Phaeosiphoniella, Phyllaria, Tilopteris.
****Class Phaeosacciophyceae → order Phaeosacciales
*****Family Phaeosaccionaceae. Genera: Antarctosaccion ; Phaeosaccion.
*****Family Tetrasporopsidaceae. Genera: Tetrasporopsis ; Psammochrysis.
****Phaeothamniophyceae
*****Phaeothamniales. Phaeothamnion.
*****Pleurochloridales. Pleurochloridella.
****Schizocladiophyceae. Schizocladia.
****Xanthophyceae
*****Tribonematales. Botrydium, Bumilleriopsis, Characiopsis, Chloromeson, Heterococcus, Monadus, Ophiocytium, Sphaerosorus, Tribonema, Xanthonema.
*****Vaucheriales. Vaucheria.
*Diatomista . Incertae sedis taxa: environmental clades MOCH-1, MOCH-2 and MOCH-4.
**Bolidophyceae . Bolidomonas, Triparma, Tetraparma, Pentalamina.
**Diatomeae
***Leptocylindrophytina
****Leptocylindrophyceae. Leptocylindrus, Tenuicylindrus.
****Corethrophyceae. Corethron.
***Ellerbeckiophytina. Ellerbeckia.
***Probosciophytina. Proboscia.
***Melosirophytina. Aulacoseira, Melosira, Hyalodiscus, Stephanopyxis, Paralia, Endictya.
***Coscinodiscophytina. Actinoptychus, Coscinodiscus, Actinocyclus, Asteromphalus, Aulacodiscus, Stellarima.
***Rhizosoleniophytina. Guinardia, Rhizosolenia, Pseudosolenia.
***Arachnoidiscophytina. Arachnoidiscus.
***Bacillariophytina
****Mediophyceae
*****Chaetocerotophycidae. Chaetoceros, Bacteriastrum, Dactyliosolen, Cerataulina, Hemiaulus, Eucampia, Acanthoceras, Urosolenia, Terpsinoë, Hydrosera.
*****Lithodesmiophycidae. Lithodesmium, Lithodesmioides, Helicotheca, Bellerochea, Ditylum.
*****Thalassiosirophycidae. Thalassiosira, Lindavia, Cyclotella, Stephanodiscus, Cyclostephanos, Discostella, Bacteriosira, Skeletonema, Detonula.
*****Cymatosirophycidae. Cymatosira, Minutocellus, Papiliocellulus, Leyanella, Extubocellulus, Plagiogrammopsis, Campylosira, Brockmanniella, Pierrecomperia.
*****Odontellophycidae. Odontella, Triceratium, Cerataulus, Pleurosira, Pseudauliscus, Amphitetras, Trieres, Mastodiscus.
*****Chrysanthemodiscophycidae. Chrysanthemodiscus, Biddulphiopsis, Trigonium, Isthmia, Lampriscus, Stictocyclus, Ardissonea, Climacosphenia, Toxarium.
****Biddulphiophyceae
*****Biddulphiophycidae. Biddulphia.
*****Attheya
****Bacillariophyceae
*****Striatellaceae. Striatella, Pseudostriatella.
*****Urneidophycidae. Plagiogramma, Dimeregramma, Rhaphoneis, Delphineis, Psammoneis, Bleakeleya, Asterionellopsis.
*****Fragilariophycidae. Fragilaria, Synedra, Tabellaria, Asterionella, Diatoma, Tabularia, Cyclophora, Astrosyne, Licmophora, Rhabdonema, Grammatophora, Staurosira, Thalassionema.
*****Bacillariophycidae. Eunotia, Achnanthes, Bacillaria, Nitzschia, Pseudonitzschia, Cylindrotheca, Navicula, Seminavis, Haslea, Pleurosigma, Gyrosigma, Achnanthidium, Cocconeis, Frustulia, Diploneis, Sellaphora, Pinnularia, Gomphonema, Cymbella, Didymosphenia, Phaeodactylum, Amphora, Entomoneis, Epithemia, Surirella, etc.
******Naviculales
*******Stauroneidaceae. Craticula, Dorofeyukea, Fistulifera, Karayevia, Madinithidium, Parlibellus, Prestauroneis, Stauroneis, Schizostauron.
**Dictyochophyceae
***Dictyochales . Dictyocha.
***Florenciellales. Florenciella, Verrucophora.
***Pedinellales . Actinomonas, Apedinella, Ciliophrys, Mesopedinella, Palatinella, Pedinella, Pseudopedinella, Pteridomonas.
***Rhizochromulinales . Rhizochromulina.
**Pelagophyceae
***Pelagomonadales. Aureococcus, Pelagococcus, Pelagomonas.
***Sarcinochrysidales
****Sarcinochrysidaceae. Ankylochrisis, Arachnochrysis, Aureoscheda, Aureoumbra, Nematochrysopsis, Pelagospilus, Pulvinaria, Sarcinochrysis, Sargassococcus.
****Chrysocystaceae. Chrysocystis, Chrysoreinhardia, Sungminbooa.
***Plocamiomonadales. Plocamiomonas.

Alveolata

Colponemida (=Protalveolata. Genera not assigned to families: Neocolponema ; Loeffela
*Phylum Colponemidia → class Colponemea → order Colponemida → family Colponemidae. Sole genus: Colponema.
*Phylum Acavomonidia → class Acavomonea → order Acavomonida → family Acavomonidae. Acavomonas.
*Order Palustrimonadida → family Palustrimonadidae. Sole genus: Palustrimonas.

Myzozoa

Phylum Chromerida → class Colpodellophyceae → order Colpodellales/Colpodellida. Incertae sedis genus: Piridium.
*Family Vitrellaceae. Sole genus: Vitrella.
*Family Colpodellaceae. Genera: Colpodella ; Chilovora ; Voromonas.
*Family Chromeraceae. Sole genus: Chromera.
*Family Alphamonadaceae/Alphamonadidae. Sole genus: Alphamonas.
Phylum Perkinsozoa → class Perkinsea. Incertae sedis genera: Phagodinium ; Rastrimonas ; Acrocoelus.
* Maranthos
*Family Pararosariidae. Sole genus: Pararosarium.
*Family Parviluciferaceae. Genera: Dinovorax ; Parvilucifera ; Snorkelia ; Tuberlatum.
*Family Perkinsidae. Sole genus: Perkinsus.
*Family Xcellidae. Genera: Cryoxcellia, Gadixcellia ; Notoxcellia ; Salmoxcellia ; Xcellia.
Phylum Dinoflagellata. Incertae sedis genera: free-living and parasitic Blastodiniales .
*Psammosa
*Family Oxyrrhinaceae. Sole genus: Oxyrrhis.
*Eleftheros
*Class Endodinea → order Ichthyodinida
**Family Hobagellidae. Sole genus: Hobagella.
**Family Euduboscquellidae. Euduboscquella ; Dogelodinium ; Keppenodinium .
**Family Ichthyodiniidae. Sole genus: Ichthyodinium.
*Class Ellobiopsea → order Ellobiopsida → family Ellobiopsidae. Genera: Ellobiopsis ; Thalassomyces ; Parallobiopsis ; Ellobiocystis ; Rhizellobiopsis.
*Class Syndiniophyceae/Syndinea → order Syndiniales
**Family Amoebophryaceae/Amoebophryidae . Sole genus: Amoebophrya.
**Family Syndiniaceae/Syndinidae . Hematodinium, Syndinium, Solenodinium.
**Family Sphaeriparaceae. Genera: Atlanticellodinium ; Sphaeripara
*Class Noctiluciphyceae → order Noctilucales. Abedinium, Cachonodinium, Craspedotella, Cymbodinium, Kofoidinium, Leptodiscus, Noctiluca, Petalodinium, Pomatodinium, Scaphodinium, Spatulodinium.
*Class Dinophyceae
**Subclass Gymnodiniphycidae
***Gymnodiniales sensu stricto. Barrufeta, Chytriodinium, Dissodinium, Erythropsidinium, Greuetodinium, Gymnodinium, Lepidodinium, Nematodinium, Nusuttodinium, Pellucidodinium, Polykrikos, Proterythropsis, Wangodinium, Warnowia.
***Amphidinium sensu stricto
***Gyrodinium sensu stricto
***Kareniaceae. Brachidinium, Karenia, Karlodinium, Takayama.
***Ceratoperidiniaceae. Ceratoperidinium, Kirithra.
***Torodiniales. Kapelodinium, Torodinium.
***Levanderina
***Margalefidinium
***Cochlodinium sensu stricto
***Ptychodiscales. Achradina, Amphilothus, Balechina, Ptychodiscus, Sclerodinium.
***Borghiellaceae. Baldinia, Borghiella.
***Tovelliaceae. Bernardinium, Esoptrodinium, Jadwigia, Tovellia.
***Suessiaceae. Ansanella, Asulcocephalium, Biecheleria, Biecheleriopsis, Leiocephalium, Pelagodinium, Polarella, Prosoaulax, Protodinium, Symbiodinium, Yihiella.
**Subclass Peridiniphycidae
***Gonyaulacales. Alexandrium, Amylax, Ceratium, Ceratocorys, Coolia, Fukuyoa, Fragilidium, Gambierdiscus, Goniodoma, Gonyaulax, Lingulodinium, Ostreopsis, Pentaplacodinium, Peridiniella, Protoceratium, Pyrocystis, Pyrodinium, Pyrophacus, Tripos.
***Peridiniales. Amphidiniopsis, Archaeperidinium, Blastodinium*, Diplopelta, Diplopsalis, Diplopsalopsis, Herdmania, Niea, Oblea, Palatinus, Parvodinium, Peridinium, Peridiniopsis, Preperidinium, Protoperidinium, Qia, Vulcanodinium.
***Thoracosphaeraceae. Aduncodinium, Amyloodinium, Apocalathium, Blastodinium, Chimonodinium, Cryptoperidiniopsis, Duboscquodinium, Ensiculifera, Laciniporus, Leonella, Luciella, Naiadinium, Paulsenella, Pentapharsodinium, Pfiesteria, Scrippsiella, Stoeckeria, Theleodinium, Thoracosphaera, Tintinnophagus, Tyrannodinium.
***Podolampadaceae. Blepharocysta, Gaarderiella, Heterobractum, Lissodinium, Mysticella, Podolampas.
***Kryptoperidiniaceae . Blixaea, Durinskia, Galeidinium, Kryptoperidinium, Unruhdinium, etc.
***Heterocapsaceae. Heterocapsa.
***Amphidomataceae. Amphidoma, Azadinium.
***Oxytoxaceae. Corythodinium, Oxytoxum.
***Centrodiniaceae. Centrodinium.
**Dinophysales. Amphisolenia, Citharistes, Dinofurcula, Dinophysis, Histioneis, Latifascia, Metadinophysis, Metaphalacroma, Ornithocercus, Oxyphysis, Parahistioneis, Phalacroma, Pseudophalacroma, Sinophysis, Triposolenia.
**Prorocentrales. Mesoporus, Prorocentrum.
Class Squirmidea. Digyalum, Filipodium, Platyproteum.
Phylum Apicomplexa. Incertae sedis genera: Aggregata, Christalloidophora, Dobellia*, Echinococcidium*, Globidiellum*, Joyeuxella*, Rhabdospora*, Spermatobium*, Spiriopsis*, Spirogregarina*, Toxocystis*, Trophosphaera*.
*Order Agamococcidiorida
**Family Gemmocystidae. Sole genus: Gemmocystis.
**Family Rhytidocystidae. Sole genus: Rhytidocystis.
*Order Protococcidiorida . Angeiocystis*, Coelotropha*, Grellia*, Eleutheroschizon*, Mackinnonia*, Myriosporides*, Myriospora*, Sawayella*.
*Aconoidasida
**Order Haemospororida. Dionisia*, Haemocystidium, Haemoproteus, Hepatocystis, Leucocytozoon, Mesnilium*, Nycteria, Parahaemoproteus, Plasmodium, Polychromophilus, Rayella*, Saurocytozoon*.
**Order Piroplasmida. Anthemosoma*, Babesia, Cytauxzoon, Echinozoon*, Haemohormidium*, Sauroplasma*, Serpentoplasma*, Theileria.
**Order Nephromycida. Nephromyces, Cardiosporidium.
*Conoidasida
**Order Corallicolida → family Corallicolidae. Genera: Corallicola ; Anthozoaphila ; Gemmocystis.
**Coccidia
***Suborder Adeleorina. Adelea*, Adelina, Babesiosima*, Bartazoon*, Chagasella*, Cyrilia*, Dactylosoma, Desseria*, Ganapatiella*, Gibbsia*, Haemogregarina, Haemolivia, Hepatozoon, Ithania*, Karyolysus, Klossia, Klossiella*, Legerella*, Orcheobius*, Rasajeyna*.
***Suborder Eimeriorina. Atoxoplasma, Barrouxia*, Besnoitia, Caryospora, Caryotropha, Choleoeimeria, Cyclospora, Cystoisospora, Defretinella*, Diaspora*, Dorisa*, Dorisiella*, Eimeria, Elleipsisoma*, Goussia, Hammondia, Hyaloklossia, Isospora, Lankesterella, Mantonella*, Merocystis, Neospora, Nephroisospora, Ovivora*, Pfeifferinella, Pseudoklossia, Sarcocystis, Schellackia, Selenococcidium*, Selysina*, Spirocystis*, Toxoplasma, Tyzzeria*, Wenyonella*.
**Gregarinida. Incertae sedis taxa: Digyalum, Exoschizon.
***Archigregarinorida . Meroselenidium, Merogregarina, Selenidium, Selenocystis, Veloxidium.
***Eugregarinorida . Apolocystis*, Amoebogregarina, Ancora, Ascogregarina, Asterophora, Blabericola, Caliculium, Cephaloidophora, Colepismatophila, Cystobia*, Cystocephalus*, Difficilina, Diplauxis*, Enterocystis, Ganymedes, Geneiorhynchus, Gonospora, Gregarina, Heliospora, Hentschelia*, Hirmocystis*, Hoplorhynchus, Lankesteria, Lecudina, Leidyana, Lithocystis, Monocystella*, Monocystis, Nematopsis, Nematocystis*, Neoasterophora*, Paralecudina, Paraschneideria, Phyllochaetopterus, Pileocephalus*, Polyplicarium, Polyrhabdina, Porospora*, Prismatospora, Protomagalhaensia, Psychodiella, Pterospora, Pyxinia, Pyxinioides, Rhabdocystis*, Sphaerorhynchus*, Steinina, Stenophora, Stylocephalus, Sycia*, Syncystis, Thalicola*, Thiriotia, Trichotokara, Uradiophora*, Urospora, Xiphocephalus, Zygosoma*, and more.
***Neogregarinorida. Apicystis, Aranciocystis, Caulleryella*, Coelogregarina*, Farinocystis*, Gigaductus*, Lipocystis*, Lipotropha*, Lymphotropha*, Machadoella*, Mattesia, Menzbieria, Ophryocystis, Schizocystis*, Syncystis, Tipulocystis*.
***Cryptogregarinorida. Cryptosporidium.
**Class Blastogregarinea. Chattonaria, Siedleckia.

Ciliophora

Postciliodesmatophora
*Karyorelictea
**Kentrophoridae. Kentrophoros.
**Loxodida
***Cryptopharyngidae. Cryptopharynx.
***Loxodidae. Loxodes.
**Geleiidae. Geleia.
*Heterotrichea
**Blepharismidae. Blepharisma
**Climacostomidae. Climacostomum.
**Condylostomatidae. Chattonidium, Condylostoma.
**Fabreidae. Fabrea.
**Gruberiidae. Gruberia.
**Coliphorina
***Folliculinidae. Folliculina.
***Maristentoridae. Maristentor.
**Peritromidae. Peritromus.
**Spirostomidae. Anigsteinia, Spirostomum.
**Stentoridae. Stentor.
Intramacronucleata. Incertae sedis taxa: Protocruziidae .
*SAL. Incertae sedis taxa: Cariacotrichea, Mesodiniidae, Phacodiniidia .
**Spirotrichea
***Euplotia
****Euplotida
*****Aspidiscidae. Aspidisca.
*****Certesiidae. Certesia.
*****Euplotidae. Euplotes.
*****Gastrocirrhidae. Gastrocirrhus.
*****Uronychidae. Diophrys, Uronychia.
****Discocephalida
*****Discocephalidae. Discocephalus, Prodiscocephalus, Paradiscocephalus.
*****Pseudoamphisiellidae. Leptoamphisiella, Pseudoamphisiella.
***Perilemmaphora
****Hypotrichia
*****Stichotrichida
******Amphisiellidae. Amphisiella, Bistichella.
******Atractosidae. Atractos.
******Epiclintidae. Epiclintes.
******Gonostomatidae. Cotterillia, Gonostomum.
******Halteriidae. Halteria, Meseres.
******Holostichidae. Holosticha, Uncinata.
******Kahliellidae. Deviata, Kahliella.
******Keronidae. Kerona.
******Oxytrichidae . Cyrtohymena, Gastrostyla, Oxytricha, Stylonychia.
******Parabirojimidae. Parabirojimia, Tunicothrix.
******Plagiotomidae. Plagiotoma.
******Psammomitridae. Psammomitra.
******Pseudoamphisiellidae. Pseudoamphisiella.
******Psilotrichidae. Psilotricha, Urospinula.
******Schmidingerotrichidae. Schmidingerothrix.
******Spirofilidae. Spirofilopsis, Strongylidium.
******Trachelostylidae. Trachelostyla.
******Uroleptidae. Paruroleptus, Uroleptus.
*****Urostylida
******Bergeriellidae. Bergeriella, Neourostylopsis.
******Hemicycliostylidae. Australothrix, Hemicycliostyla.
******Pseudokeronopsidae. Apoholosticha, Pseudokeronopsis.
******Pseudourostylidae. Pseudourostyla.
******Urostylidae. Bakuella, Diaxonella, Urostyla.
****Oligotrichea
*****Oligotrichida
******Cyrtostrombidiidae. Cyrtostrombidium.
******Pelagostrombidiidae. Pelagostrombidium.
******Strombidiidae. Strombidium.
******Tontoniidae. Laboea, Tontonia.
*****Choreotrichida. Incertae sedis taxa: Lynnella
******Strobilidiina
*******Leegaardiellidae. Leegaardiella.
*******Lohmanniellidae. Lohmanniella.
*******Strobilidiidae. Strobilidium.
*******Strombidinopsidae. Strombidinopsis.
******Tintinnina. Incertae sedis taxa: Helicostomella, Tintinnopsis, several other genera.
*******Ascampbelliellidae. Ascampbelliella
*******Cyttarocylididae . Cyttarocylis.
*******Dictyocystidae. Dictyocysta.
*******Epiplocylididae. Epiplocylis.
*******Eutintinnidae. Dartintinnus, Eutintinnus.
*******Favellidae. Favella.
*******Nolaclusiliidae. Nolaclusilis.
*******Petalotrichidae . Petalotricha.
*******Ptychocylididae. Cymatocylis, Ptychocylis.
*******Rhabdonellidae. Metacylis, Rhabdonella, Schmidingerella.
*******Stenosemellidae . Stenosemella.
*******Tintinnidae. Amphorellopsis, Salpingacantha, Salpingella, Tintinnus.
*******Tintinnidiidae. Tintinnidium.
*******Undellidae. Undella.
*******Xystonellidae. Dadayiella, Parafavella, Xystonella.
***Licnophoridae. Licnophora, Prolicnophora.
***Kiitrichidae. Caryotricha, Kiitricha.
**Lamellicorticata
***Armophorea. Incertae sedis taxa: Mylestomatidae .
****Metopida
*****Metopidae . Bothrostoma, Brachonella, Eometopus, Metopus, Parametopidium, Tesnospira.
*****Apometopidae. Cirranter, Urostomides.
*****Tropidoatractidae. Palmarella, Tropidoatractus.
****Clevelandellida
*****Clevelandellidae. Clevelandella.
*****Inferostomatidae. Inferostoma.
*****Neonyctotheridae. Neonyctotherus.
*****Nyctotheridae . Nyctotherus.
*****Sicuophoridae. Sicuophora.
****Caenomorphidae. Caenomorpha, Ludio, Sulfonecta.
****Odontostomatida
*****Discomorphellidae. Discomorphella.
*****Epalxellidae. Epalxella, Saprodinium.
***Litostomatea
****Rhynchostomatia
*****Dileptida
******Dileptidae. Apodileptus, Dileptus, Pseudomonilicaryon.
******Dimacrocaryonidae. Dimacrocaryon, Monomacrocaryon, Rimaleptus.
******Tracheliidae. Trachelius.
****Haptoria . Incertae sedis taxa: Chaenea.
*****Lacrymariidae. Lacrymaria.
*****Haptorida
******Enchelyodonidae. Enchelyodon, Fuscheria.
******Homalozoonidae. Homalozoon.
******Pleuroplitidae. Pleuroplites.
*****Didiniidae. Didinium, Monodinium.
*****Pleurostomatida
******Amphileptidae. Amphileptus.
******Litonotidae. Litonotus.
******Kentrophyllidae. Epiphyllum, Kentrophyllum.
*****Spathidiida
******Acropisthiidae. Acropisthium, Chaenea.
******Actinobolinidae. Actinobolina.
******Apertospathulidae. Apertospathula.
******Enchelyidae. Enchelys.
******Pseudoholophryidae. Pseudoholophrya.
******Spathidiidae. Legendrea, Spathidium.
******Trachelophyllidae. Trachelophyllum.
*****Helicoprorodontidae
****Trichostomatia
*****Vestibuliferida
******Balantidiidae. Balantidium, Neobalantidium.
******Buetschliidae. Buetschlia.
******Paraisotrichidae. Paraisotrichia.
******Protocaviellidae. Protocaviella.
******Protohalliidae. Protohallia.
******Pycnotrichidae. Pycnothrix, perhaps Buxtonella.
****Isoendo
*****Isotrichidae. Dasytricha, Isotricha.
*****Entodiniomorphida
******Blepharocorythina
*******Blepharocorythidae. Blepharocorys.
*******Parentodiniidae. Parentodinium.
*******Pseudoentodiniidae. Pseudoentodinium.
******Entodiniomorphina
*******Cycloposthiidae. Cycloposthium.
*******Gilchristinidae . Digilchristia, Gilchristina.
*******Ophryoscolecidae. Entodinium, Ophryoscolex, Polyplastron.
*******Polydiniellidae. Polydiniella.
*******Rhinozetidae. Rhinozeta.
*******Spirodiniidae. Spirodinium.
*******Telamodiniidae. Telamodinium.
*******Troglodytellidae. Troglodytella,.
*****Macropodiniida
******Amylovoracidae. Amylovorax.
******Macropodiniidae. Macropodinium.
******Polycostidae. Polycosta.
*CONTHREEP . Incertae sedis taxa: Askenasia, Cyclotrichiidae, Paraspathidium, Pseudotrachelocercidae, Discotrichidae .
**Phyllopharyngea
***Synhymeniida
****Nassulopsidae. Nassulopsis.
****Orthodonellidae. Orthodonella, Zosterodasys.
****Scaphidiodontidae. Chilodontopsis, Scaphidiodon.
****Synhymeniidae. Synhymenia.
***Subkinetalia
****Cyrtophoria
*****Chlamydodontida
******Chilodonellidae. Chilodonella.
******Chitonellidae. Chitonella.
******Chlamydodontidae. Chlamydodon.
******Gastronautidae. Gastronauta.
******Kryoprorodontidae. Gymnozoum.
******Lynchellidae. Chlamydonella, Lynchella.
*****Dysteriida
******Dysteriidae. Dysteria, Trochilia.
******Hartmannulidae . Hartmannula.
******Kyaroikeidae. Kyaroikeus.
******Plesiotrichopidae. Plesiotrichopus.
******Chonotrichia
*******Exogemmida
********Chilodochonidae. Chilodochona.
********Filichonidae. Filichona.
********Helichonidae. Heliochona.
********Lobochonidae. Lobochona.
********Phyllochonidae. Phyllochona.
********Spirochonidae. Spirochona.
*******Cryptogemmida
********Actinichonidae. Actinichona.
********Echinichonidae. Echinichona.
********Inversochonidae. Inversochona.
********Isochonidae. Isochona.
********Isochonopsidae. Isochonopsis.
********Stylochonidae. Stylochona.
****Rhynchodia
*****Hypocomidae. Hypocoma.
*****Rhynchodida
******Ancistrocomidae. Ancistrocoma.
******Sphenophryidae. Sphenophrya.
****Suctoria
*****Exogenida
******Allantosomatidae. Allantosoma.
******Dentacinetidae. Dentacineta.
******Dendrosomididae. Dendrosomides.
******Ephelotidae. Ephelota.
******Lecanophryidae. Lecanophrya.
******Manuelophryidae. Manuelophrya.
******Metacinetidae. Metacineta.
******Ophryodendridae. Ophryodendron.
******Paracinetidae. Paracineta.
******Phalacrocleptidae. Phalacrocleptes.
******Podophryidae. Podophrya.
******Praethecacinetidae. Praethecacineta.
******Rhabdophryidae. Rhabdophrya.
******Severonidae. Severonis.
******Spelaeophryidae. Spelaeophrya.
******Tachyblastonidae. Tachyblaston.
******Thecacinetidae. Thecacineta.
*****Endogenida
******Acinetidae. Acineta.
******Acinetopsidae. Acinetopsis.
******Choanophryidae. Choanophrya.
******Corynophryidae. Corynophrya.
******Dactylostomatidae. Dactylostoma.
******Dendrosomatidae. Dendrosoma.
******Endosphaeridae. Endosphaera.
******Erastophryidae. Erastophrya.
******Pseudogemmidae. Pseudogemma.
******Rhynchetidae. Rhyncheta.
******Solenophryidae. Solenophrya.
******Tokophryidae. Tokophrya.
******Trichophryidae. Trichophrya.
*****Evaginogenida
******Cometodendridae. Cometodendron.
******Cyathodiniidae. Cyathodinium.
******Dendrocometidae. Dendrocometes.
******Discophryidae. Discophrya.
******Enchelyomorphidae. Enchelyomorpha.
******Heliophryidae. Heliophrya.
******Periacinetidae. Periacineta.
******Prodiscophryidae. Prodiscophrya.
******Rhynchophryidae. Rhynchophrya.
******Stylocometidae. Stylocometes.
******Trypanococcidae. Trypanococcus.
**Colpodea
***Bursariomorphida
****Bryometopidae. Bryometopus (P), Thylakidium.
****Bursaridiidae. Bursaridium, Paracondylostoma.
****Bursariidae. Bursaria.
***Colpodida. Incertae sedis taxa: Bardeliellidae, Hausmanniellidae, Ilsiellidae, Pseudochlamydonellidae and Marynidae .
****Bryophryina
*****Bryophryidae. Bryophrya.
*****Sandmanniellidae. Sandmanniella.
****Colpodina
*****Colpodidae . Colpoda.
*****Grandoriidae. Grandoria.
*****Tillinidae. Tillina.
****Grossglockneriidae . Grossglockneria, Pseudoplatyophrya.
***Cyrtolophosidida
****Cyrtolophosididae. Cyrtolophosis.
****Kreyellidae. Kreyella.
***Platyophryida
****Ottowphryidae. Ottowphrya, Platyophryides.
****Platyophryidae . Platyophrya.
****Sagittariidae. Sagittaria.
****Sorogenidae. Sorogena.
****Woodruffiidae. Etoschophrya, Rostrophrya, Woodruffia.
**Nassophorea
***Colpodidiidae. Colpodidium.
***Nassulida
****Furgasoniidae. Furgasonia, Wolfkosia.
****Nassulidae. Nassula, Obertrumia.
***Microthoracida
****Microthoracidae. Drepanomonas, Microthorax.
****Leptopharyngidae. Leptopharynx, Pseudomicrothorax.
**Prostomatea
***Apsiktratidae
****Balanionidae. Balanion.
****Cryptocaryonidae. Cryptocaryon.
****Colepidae. Coleps, Plagiopogon.
****Holophryidae. Holophrya.
****Lagynidae. Lagynus.
****Metacystidae. Metacystis, Vasicola.
****Placidae. Placus.
****Plagiocampidae. Plagiocampa.
****Prorodontidae. Prorodon.
****Urotrichidae. Urotricha.
**Plagiopylea
***Plagiopylida
****Epalxellidae. Epalxella, Saprodinium.
****Plagiopylidae. Plagiopyla.
****Sonderiidae. Sonderia.
****Trimyemidae. Trimyema.
**Oligohymenophorea
***Apostomatia
****Apostomatida
*****Colliniidae. Collinia, Metacollinia.
*****Cyrtocaryidae. Cyrtocaryum.
*****Foettingeriidae. Foettingeria.
*****Pseudocolliniidae. Fusiforma, Pseudocollinia.
****Astomatophorida
*****Opalinopsidae. Opalinopsis.
****Pilisuctorida
*****Conidophryidae. Conidophrys.
***Astomatia
****Anoplophryidae. Anoplophrya.
****Buetschliellidae. Buetschliella.
****Clausilocolidae. Clausilocola.
****Contophryidae. Contophyra.
****Haptophryidae. Haptophrya.
****Hoplitophryidae. Hoplitophrya.
****Intoshellinidae. Intoshellina.
****Maupasellidae. Maupasella.
****Radiophryidae. Radiophrya.
***Hymenostomatia
****Tetrahymenida. Incertae sedis taxa: Trichospiridae .
*****Curimostomatidae. Curimostoma.
*****Glaucomidae. Glaucoma.
*****Spirozonidae. Spirozona.
*****Tetrahymenidae. Tetrahymena.
*****Turaniellidae. Colpidium, Dexiostoma, Turaniella.
****Ophryoglenida
*****Ichthyophthiriidae. Ichthyophthirius.
*****Ophryoglenidae. Ophryoglena.
***Peniculia
****Peniculida
*****Clathrostomatidae. Clathrostoma.
*****Frontoniidae. Disematostoma, Frontonia.
*****Lembadionidae. Lembadion.
*****Maritujidae. Marituja.
*****Neobursaridiidae. Neobursaridium.
*****Parameciidae. Paramecium.
*****Paranassulidae. Paranassula.
*****Stokesiidae. Stokesia.
*****Urocentridae
***Peritrichia
****Sessilida
*****Astylozoidae. Astylozoon, Hastatella.
*****Ellobiophryidae. Ellobiophrya.
*****Epistylididae. Epistylis.
*****Lagenophryidae. Lagenophrys.
*****Operculariidae. Opercularia.
*****Rovinjellidae. Rovinjella.
*****Scyphidiidae . Scyphidia.
*****Termitophryidae. Termitophrya.
*****Usconophryidae. Usconophrys.
*****Vaginicolidae. Cothurnia, Pyxicola, Thuricola, Vaginicola.
*****Vorticellidae. Carchesium, Epicarchesium, Ophrydium, Pelagovorticella, Pseudovorticella, Vorticella.
*****Zoothamniidae. Haplocaulus, Zoothamnium.
****Mobilida
*****Polycyclidae. Polycycla.
*****Trichodinidae. Trichodina.
*****Trichodinopsidae. Trichodinopsis.
*****Urceolariidae. Leiotrocha, Urceolaria.
***Scuticociliatia
****Philasterida
*****Cohnilembidae. Cohnilembus.
*****Cryptochilidae. Cryptochilum.
*****Entodiscidae. Entodiscus.
*****Entorhipidiidae. Entorhipidium.
*****Orchitophryidae . Orchitophrya.
*****Paralembidae. Anophrys, Paralembus.
*****Parauronematidae . Parauronema.
*****Philasteridae. Kahlilembus, Philaster.
*****Pseudocohnilembidae. Pseudocohnilembus.
*****Schizocaryidae. Schizocaryum.
*****Thigmophryidae. Thigmophrya.
*****Thyrophylacidae. Thyrophylax.
*****Uronematidae. Uronema.
*****Urozonidae. Urozona.
****Pleuronematida
*****Calyptotrichidae. Calyptotricha.
*****Conchophthiridae. Conchophthirus.
*****Ctedoctematidae. Ctedoctema.
*****Cyclidiidae . Cristigera, Cyclidium.
*****Dragescoidae. Dragescoa.
*****Eurystomatellidae. Eurystomatella.
*****Histiobalantiidae. Histiobalantium.
*****Peniculistomatidae. Peniculistoma.
*****Pleuronematidae . Pleuronema.
*****Thigmocomidae. Thigmocoma.
****Thigmotrichida
*****Ancistridae. Ancistrum.
*****Hemispeiridae. Hemispeira.
*****Hysterocinetidae. Hysterocineta.
*****Paraptychostomidae. Paraptychostomum.
****Loxocephalida
*****Cinetochilidae . Cinetochilum, Sathrophilus.
*****Loxocephalidae. Cardiostomatella, Dexiotricha, Loxocephalus.

Rhizaria

Incertae sedis taxa: Gymnosphaerida. Actinocoryne, Cienkowskya, Gymnosphaera, Hedraiophrys, Wagnerella.

Cercozoa

Incertae sedis taxa:
*Aquavolonida. Aquavolon, Lapot.
*Tremulida. Tremula.
* Genera of uncertain placement: Dictiomyxa, Katabia, Myxodictyium, Pontomyxa, Protomyxa, Protogenes, Pseudospora, Rhizoplasma
* Discocelia
* Psammonobiotidae*. Alepiella, Chardezia, Edaphonobiotus, Feuerbornia, Frenzelina, Lesquerella, Micramphora, Micropsammella, Nadinella, Ogdeniella, Psammonobiotus, Propsammonobiotus, Rhumbleriella.
Sarcomonadea
*Order Cercomonadida, family Cercomonadidae, genera Cercomonas, Eoercomonas, Filomonas, Neocercomonas, Cavernomonas.
*Paracercomonadida . Brevimastigomonas, Metabolomonas, Nucleocercomonas, Paracercomonas, Phytocercomonas.
*Glissomonadida
**Saccharomycomorphidae. Saccharomycomorpha.
**Sandonidae. Sandona, Flectomonas, Neoheteromita, Mollimonas.
**Dujardinidae. Dujardina.
**Bodomorphidae. Bodomorpha.
**Proleptomonadidae. Proleptomonas.
**Allapsidae. Allapsa, Teretomonas, Allantion.
**Viridiraptoridae. Orciraptor, Viridiraptor.
**Pansomonadidae. Agitata, Aurigamonas.
Sainouroidea
*Sainouridae. Acantholus, Cholamonas, Homocognata, Sainouron.
*Helkesimastigidae. Helkesimastix.
*Guttulinopsidae. Guttulinopsis, Olivorum, Puppisaman, Rosculus.
Thecofilosea. Incertae sedis taxa: Mataza.
*Phaeodarea
**Phaeoconchia. Coelodendrum, Coelographis, Conchellium, Conchopsis.
**Phaeocystina. Aulacantha, Aulographis, Cannoraphis.
**Phaeogromia. Castanella, Challengeron, Haeckeliana, Medusetta, Tuscarora.
**Phaeosphaeria. Aulosphaera, Cannosphaera, Sagosphaera.
*Cryomonadida
**Rhogostomidae. Rhogostoma, Sacciforma, Capsellina.
**Protaspidae . Cryothecomonas, Protaspa.
*Ventricleftida
**Ventrifissuridae. Ventrifissura.
**Verrucomonadidae. Verrucomonas.
*Tectofilosida
**Chlamydophryidae. Chlamydophrys, Diaphoropodon, Lecythium, Katarium, Trachyrhizium.
**Psammonobiotidae. Micropsamella.
**?Volutellidae. Pseudovolutella, Volutella.
**Fiscullina
***Fiscullidae. Fisculla, Omnivora.
***Pseudodifflugiidae. Pseudodifflugia.
***Rhizaspididae. Rhizaspis.
*Ebriacea . Ebria, Hermesinum, Botuliforma.
Imbricatea
*Spongomonadida . Rhipidodendron, Spongomonas.
*Marimonadida
**Abolliferidae. Abollifer, Cowlomonas, ?Heterochromonas.
**Auranticordidae. Auranticordis, Rhabdamoeba.
**Cyranomonadidae. Cyranomonas.
**Pseudopirsoniidae. Pseudopirsonia.
*Variglissida
**Clautriaviidae. Clautriavia.
**Nudifilidae. Nudifila.
**Quadriciliidae. Quadricilia.
*Silicofilosea
**Thaumatomonadida
***Thaumatomonadidae. Allas, Hyaloselene, Reckertia, Thaumatomonas, Thaumatomastix, Ovaloplaca, Scutellomonas, Thaumatospina, Penardeugenia.
***Peregriniidae. Gyromitus, Peregrinia.
***Esquamulidae. Esquamula.
**Euglyphida. Incertae sedis taxa: Phaeobola.
***Cyphoderiidae. Campascus*, Corythionella, Cyphoderia, Messemvriella*, Pseudocorythion, Ichthyosquama, Knarr, Oleiformis, Psammoderia.
***Paulinellidae. Micropyxidiella, Ovulinata, Paulinella.
***Euglyphina
****Assulinidae. Assulina, Placocista, Valkanovia*.
****Sphenoderiidae. Sphenoderia, Trachelocorythion, Deharvengia*.
****Trinematidae. Corythion, Playfairina*, Puytoracia*, Trinema.
****Euglyphidae. Euglypha, Scutiglypha.
****Tracheleuglypha
**Trivalvulariida. Leptogromia, Trivalvularis.
Metromonadea. Metromonas, Metopion, Micrometopion, Kiitoksia.
Granofilosea. Incertae sedis taxa*: ?Apogromia, ?Kibisidytes, ?Leucodictyon, ?Limnofila, ?Mesofila, ?Microcometes, ?Microgromia, ?Nanofila, ?Reticulamoeba and probably ?Belaria, ?Ditrema, ?Heliomorpha and ?Paralieberkuehnia.
*Massisteridae. Massisteria, Minimassisteria.
*Clathrulinidae . Actinosphaeridium, Cienkowskya*, Clathrulina, Hedriocystis, Penardiophrys, ?Servetia.
Chlorarachnea. Amorphochlora, Bigelowiella, Chlorarachnion, Cryptochlora, Gymnochlora, Lotharella, Minorisa, Partenskyella, Viridiuvalis.

Endomyxa

Vampyrellida . Incertae sedis taxa: Arachnula, Gobiella, Lateromyxa, Penardia.
*Thalassomyxa
*Vampyrellidae. Vampyrella.
*Leptophryidae. Arachnomyxa, Leptophrys, Planctomyxa, Platyreta, Pseudovampyrella, Theratromyxa, Vernalophrys.
*Placopodidae . Placopus.
*Sericomyxidae. Sericomyxa.
Phytomyxea
*Marinomyxa
*Plasmodiophorida . Plasmodiophora, Polymyxa, Woronina, Ligniera, Sorosphaerula, Spongospora, ?Membranosorus, ?Octomyxa, ?Polymyxa, ?Sorodiscus, ?Tetramyxa .
*Phagomyxida. Phagomyxa, Maullinia.
Filoreta
Gromia
Viscidocauda
Ascetosporea
*Haplosporida. Bonamia, Haplosporidium, Minchinia, Urosporidium.
*Mikrocytida. Mikrocytos, Paramikrocytos.
*Paramyxida. Marteilia, Paramyxa, Paramarteilia, Marteilioides, Eomarteilia.
*Claustrosporidium
*Paradiniida. Paradinium.

Retaria

Foraminifera

Subphylum Foraminifera

Lagenida
Heterogromia
Komokiacea*
'Monothalamids' . Genera not assigned to any lower taxon: Astrammina, Crithionina, Notodendrodes, Psammophaga, Bathysiphon, Nujappikia.
*Family Lieberkuehniidae, genera Lieberkuehnia, Claparedellus.
*Family Edaphoallogromiidae, sole genus Edaphoallogromia.
*Family Lacogromiidae, sole genus Lacogromia.
*Family Limnogromiidae, sole genus Limnogromia.
*Family Reticulomyxidae. Reticulomyxa, Dracomyxa, Haplomyxa, Wobo.
*Family Schizamminidae, genera Jullienella, Schizammina, Spiculosiphon.
*Family Velamentofexidae, sole genus Velamentofex.
*Order Allogromiida
**Family Allogromiidae, genera Allogromia, Vellaria.
*Order Astrorhizida
**Superfamily Xenophyophoroidea
Class Tubothalamea. Fusulinida probably belongs to this group.
*Order Miliolida. Alveolina, Cornuspira, Miliammina, Pyrgo, Quinqueloculina, Sorites.
*Order Spirillinida. Patellina, Spirillina.
*Family Ammodiscidae. Ammodiscus, Glomospira.
Class Globothalamea
*Order Rotaliida
**Family Planorbulinidae. Planorbulinella, Hyalinea.
**Superfamily Discorboidea
***Family Discorbidae. Discorbis.
***Family Rosalinidae. Rupertina, Discanomalina, "Rosalina", Gavelinopsis, Planorbulina.
**Superfamily Rotalioidea. Incertae sedis taxa: ?Criboelphidium, ?"Elphidium", ?Protelphidium.
***Family Elphidiidae. Elphidium.
***Family Ammoniidae. Ammonia.
***Family Elphidiellidae. Elphidiella.
***Family Haynesinidae. Haynesina, Aubignyna.
**Superfamily Glabratelloidea
***Family Rotaliellidae. Rotaliella, Rossyatella.
***Family Buliminoididae. Buliminoides.
***Family Glabratellidae. Glabratella, Glabratellina, Angulodiscorbis, Planoglabratella.
**Superfamily Calcarinoidea
***Family Calcarinidae. Neorotalia, Baculogypsina, Baculogypsinoides, Schlumbergerella, Pararotalia.
**Superfamily Nummulitoidea, family Nummulitidae. Nummulites, Operculinella, Cycloclypeus, Heterostegina, Operculina, Planoperculina, Planostegina.
**Superfamily Serioidea
***Family Uvigerinidae. Uvigerina, Rectuvigerina, Trifarina.
***Family Bolivinitidae. Bolivina, Brizalina, Saidovina.
***Family Cassidulinidae. Globocassidulina, Cassidulinoides, Evolvocassidulina, Islandiella, Ehrenbergina
***Family Sphaeroidinidae. Sphaeroidina.
***Family Globobuliminidae. Globobulimina.
**Incertae sedis families
***Family Nonionidae. Nonion, Nonionella, Nonionellina, Nonionoides.
***Family Virgulinellidae. Virgulinella.
***Family Buliminidae. Bulimina.
***Family Epistominellidae. Epistominella.
***Family Stainforthiidae. Stainforthia, Gallitellia.
***Family Cibicididae. Cibicides, Cibicidoides, Heterolepa.
***Family Chilostomellidae. Chilostomella.
***Family Pullenidae. Pullenia.
***Family Nuttalidae. Nuttalides.
***Family Discorbinellidae. Discorbinella, Hanzawaia.
***Family Astrononionidae. Astrononion.
***Family Oridorsalidae. Oridorsalis.
***Family Melonidae. Melonis.
***Family Cymbaloporidae. Cymbaloporella.
***Family Rubratelliidae. Rubratella.
***Family Murrayinelliidae. Murrayinella.
*Order Globigerinida
**Superfamily Parvularugoglobigerinoidea
***Family Parvularuglobigerinidae. Pseudocaucasina, Palaeoglobigerina, Parvularugoglobigerina.
**Superfamily Eoglobigerinoidea
***Family Eoglobigerinidae. Alicantina, Eoclavatorella, Eoglobigerina, Parasubbotina, Pseudoglobigerinella, Subbotina, Turbeogloborotalia.
***Family Globoquadrinidae. Dentoglobigerina, Globoquadrina.
***Family Neoacarininidae. Neoacarinina.
***Family Porticulasphaeridae. Globigerinatheka, Guembelitrioides, Inordinatosphaera, Orbulinoides, Porticulasphaera.
**Superfamily Globigerinoidea
***Family Globigerinidae. Alloglobigerinoides, Ciperoella, Globigerina, Globicuniculus, Globigerinoides, Globigerinoidesella, Globoturborotalita, Trilobigerina, Zeaglobigerina.
***Family Globigerinellidae. Beella, Bolliella, Globigerinella, Orcadia, Protentella, Quiltyella.
***Family Hastigerinidae. Hastigerina, Hastigerinella, Hastigerinopsis.
***Family Orbulinidae. Biorbulina, Candorbulina, Orbulina, Praeorbulina.
***Family Sphaeroidinellidae. Prosphaeroidinella, Sphaeroidinella, Sphaeroidinellopsis.
***Family Turborotalitidae. Berggrenia, Turborotalita.
**Superfamily Globorotalioidea
***Family Catapsydracidae. Catapsydrax, Globigerinopsoides, Globigerinoita, Velapertina.
***Family Globorotaloididae. Clavatorella, Globorotaloides, Protentelloides.
***Family Globorotaliidae. Dentigloborotalia, Globoconella, Globorotalia, Hirsutella, Jenkinsella, Menardella, Neogloboquadrina, Paragloborotalia, Truncorotalia.
***Family Pulleniatinidae. Pulleniatina.
**Superfamily Globanomalinidoidea, family Globanomalinidae. Carinoturborotalia, Globanomalina, Luterbacheria, Planoglobanomalina, Turborotalia.
**Superfamily Hantkeninoidea
***Family Pseudohastigerinidae. Pseudohastigerina.
***Family Hantkeninidae. Applinella, Aragonella, Clavigerinella, Cribrohantkenina, Hantkenina.
**Superfamily Truncorotaloidinoidea
***Family Globigerapsidae. Globigerapsis, Muricoglobigerina.
***Family Planorotalitidae. Astrorotalia, Planorotalites.
***Family Truncorotaloididae. Acarinina, Igorina, Morozovella, Morozovelloides, Pearsonites, Praemurica, Pseudogloboquadrina, Testacarinata, Truncorotaloides.
*Order Globotruncanida
**Superfamily Abathomphaloidea
***Family Abathomphalidae. Abathomphalus.
***Family Globotruncanellidae. Globotruncanella, Spinoglobotruncanella.
**Superfamily Favuselloidea
***Family Conoglobigerinidae. Conoglobigerina, Tenuigerina, ?Sphaerogerina.
***Family Favusellidae. Ascoliella, Favusella, Koutsoukosia.
***Family Globuligerinidae. Compactogerina, Globuligerina, Haeuslerina, Petaloglobigerina.
**Superfamily Hedbergelloidea
***Family Ananiidae. Anania, Badriella, Costellagerina, Hillsella, Liuenella, Loeblichella, Muricohedbergella, Paracostellagerina, Pessagnoina, Planohedbergella, Pseudoclavihedbergella, Vanhintella.
***Family Hedbergellidae. Asterohedbergella, Clavihedbergella, Hedbergella, Microhedbergella, Paraticinella, Pseudoguembelitria.
***Family Helvetoglobotruncanidae. Angulocarinella, Bermudeziana, Bollitruncana, Fingeria, Hedbergellita, Brittonella, Helvetoglobotruncana, Unitruncatus, Whiteinella.
***Family Praehedbergellidae. Blefuscuiana, Gorbachikella, Praehedbergella, Lilliputianella, Lilliputianelloides, Wondersella.
**Superfamily Globotruncanoidea
***Family Globotruncanidae. Contusotruncana, Globotruncana, Marginotruncana, Obliquacarinata, Sphaerotruncana, Ventrotruncana.
***Family Praeglobotruncanidae. Concavatotruncana, Dicarinella, Falsotruncana, Rotundina, Praeglobotruncana, Verotruncana.
***Family Reissidae. Elevatotruncana, Globotruncanita, Kassabiana, Radotruncana, Sigalitruncana, Turbotruncana.
**Superfamily Planomalinoidea
***Family Eohastigerinellidae. Eohastigerinella, Hastigerinoides.
***Family Globigerinelloididae. Alanlordella, Allotheca, Biglobigerinella, Blowiella, Claviblowiella, Globigerinelloides, Pseudoschackoina.
***Family Planomalinidae. Bannerina, Planomalina, Pseudoplanomalina.
***Family Schackoinidae. Asymetria, Groshenyia, Leupoldina, Neoschackoina, Schackoina.
**Superfamily Rotaliporoidea
***Family Rotaliporidae. Anaticinella, Pseudothalmanninella, Rotalipora, Thalmanninella.
***Family Ticinellidae. Biticinella, Claviticinella, Ticinella.
**Superfamily Rugoglobigerinoidea
***Family Helvetiellidae. Archaeoglobigerina, Bucherina, Dorbignya, Edgarinella, Gandolfia, Gansserina, Globocarinata, Helvetiella, Kuglerina.
***Family Rugoglobigerinidae. Archaeoglobitruncana, Plummerita, Rugoglobigerina, Rugosocarinata, Rugotruncana, Trinitella.
*Order Heterohelicida
**Superfamily Heterohelicoidea
***Family Gublerinidae. Gublerina, Lipsonia, Praegublerina.
***Family Heterohelicidae. Braunella, Bronnimannella, Ehrenbergites, Globoheterohelix, Fleisherites, Hartella, Heterohelix, Huberella, Laeviheterohelix, Lazarusina, Lunatriella, Magellanina, Mihaia, Nederbragtina, Planoheterohelix, Protoheterohelix, Pseudoplanoglobulina, Steineckia, Striataella, Texasina, ?Bifarina, ?Rectoguembelina, ?Zeauvigerina.
***Family Pseudotextulariidae. Planoglobulina, Pseudotextularia, Racemiguembelina.
***Family Pseudoguembelinidae. Eicheriella, Leptobimodalia, Pseudoguembelina.
***Family Spiroplectidae. Hendersonites, Neohendersonites, Paraspiroplecta, Spiroplecta.
***Family Ventilabrellidae. Planulitella, Proliferania, Sigalia, Ventilabrella.
*Order Guembelitriida
**Superfamiily Cassigerinelloidea, family Cassigerinellidae. Cassigerinella, Riveroinella.
**Superfamily Guembelitrioidea, family Guembelitriidae. Cassigerinelloita, Guembelitria, Chiloguembelitria, Jenkinsina, ?Archaeoguembelitria, ?Gallitellia, ?Guembelitriella.
**Superfamily Chiloguembelinoidea, family Chiloguembelinidae. Chiloguembelina, Woodringina, ?Streptochilus.
**Superfamily Globoconusoidea, family Globoconusidae. Globoconusa, Trochoguembelitria,
*Order ?
**Superfamily Globigerinitoidea
***Family Candeinidae. Candeina.
***Family Globigerinatellidae. Globigerinatella.
***Family Globigerinitidae. Globigerinita, Mutabella, Polyperibola, Tinophodella.
***Family Tenuitellidae. Praetenuitella, Tenuitella, Tenuitellinata, Tenuitellita.
***Family ?. Dipsidripella, ?Antarcticella.
*Order Robertinida. Hoeglundina, Robertina, Robertinoides.
*Order Textulariida. Cyclammina, Eggerella, Reophax, Textularia, Trochammina.
*Order Carterinida. Carterina.

Radiolaria

Radiolaria
*Acantharea
**Chaunocanthida. Amphiacon, Conacon, Gigartacon, Heteracon, Stauracon.
**Holocanthida. Acanthochiasma, Acanthocolla, Acanthoplegma.
**Symphyacanthida. Amphilithium, Astrolonche, Pseudolithium.
**Arthracanthida. Acanthometra, Daurataspis, Dictyacantha, Diploconus, Phractopelta, Phyllostaurus, Pleuraspis, Stauracantha.
*Taxopodida. Sticholonche.
*Polycystinea
**Spumellaria
***Hexacromyoidea
****Hexacaryidae : Clevepilegma, Haliphormis, Hexacaryum, Hexalonchetta, Hexancistra, Hexapitys.
****Hexacromyidae : Carpocanthum, Hexacromyum, Hexalonchilla, Nanina .
****Hollandosphaeridae : Anomalosoma, Tetrapetalon.
***Spongosphaeroidea → Spongosphaeridae : Diplospongus, Spongodendron, Spongosphaera .
***Lithocyclioidea
****Astracturidae : Astromma, Amphactura, Hymeniastrum .
****Lithocycliidae : Cromyatractus, Heliosestrum ; Heliostylus, Lithocyclia, Phacostaurus, Phacotriactis, Sethostylus, Staurocyclia, Triactiscus .
****Panartidae : Cannartus, Diartus, Didymocyrtis, Spongolivella.
****Phacodiscidae : Periphaena, Phacodiscus .
***Spongodiscoidea
****Spongodiscidae : Spongaster, Spongodiscus, Spongotrochus .
****Euchitoniidae : Amphicraspedum, Dictyocoryne, Hexinastrum, Ommatocampe, Tessarastrum, Tricanastrum, Trigonastrum .
****Spongobrachiidae : Spongasteriscus, Spongastromma, Spongobrachium.
***Cladococcoidea
****Ethmosphaeridae : Cyrtidosphaera, Ethmosphaera,, Haplosphaera, Heliosphaera, Liosphaera .
****Cladococcidae : Arachnosphaera, Arachnospongus, Cladococcus, Diplosphaera, Haeckeliella, Lychnosphaera .
***Trematodiscoidea → Trematodiscidae : Flustrella, Staurospira, Stylodictya, Tripodictya .
***Haliommoidea
****Actinommidae : Actinomma, Cromyechinus, Rhaphidocapsa, Sphaeractis, Staurocaryum, Stomatosphaera, Stuermeria.
****Haliommidae : Cromyosphaera, Haliomma, Haliommantha, Hexacontella, Melittosphaera, Pseudostaurosphaera .
****Heliodiscidae : Actinommura, Excentrococcus, Excentrodiscus, Heliodiscus, Helioferrusa, Phaenicosphaera .
***Lithelioidea
****Conocaryommidae : Conocaryomma .
****Litheliidae : Lithelius, Middourium, Spiremaria, Spongocyclia .
****Phaseliformidae : Phaseliforma.
****Pyramispongiidae : Pyramispongia .
****Sponguridae : Ommatogramma .
***Spongopyloidea
****Spongopylidae : Schizodiscus, Spongobrachiopyle, Spongopyle, Spongospira.
****Cristallosphaeridae : Calcaromma, Enalomelon.
****Prunopylidae : Prunopyle, Spongopylidium.
***Phorticioidea
****Amphitholidae
****Circodiscidae
****Cryptolarnaciidae
****Histiastridae
****Phorticiidae
***Larcospiroidea
****Dipylissidae
****Larcospiridae
****Palaeotetrapylidae
****Pylodiscidae
****Zonariidae
***Pseudoaulophacoidea
****Patulibracchiidae
****Pseudoaulophacidae
****Suttoniidae
***Stylosphaeroidea
****Entapiidae
****Stylatractidae
****Tubosphaeridae
**Nassellaria. Artostrobus, Eucyrtidium, Lithomelissa, Pterocanium, Pterocorys.
**Collodaria. Acrosphaera, Collosphaera, Collozoum, Sphaerozoum, Rhaphidozoum, Siphonsphaera, Thalassicolla.
**Orodaria
***Oroscenidae . Oroscena, Orostaurus, Oropelex. Nomina dubia genera: Orosphaera, Orodictyum, Orona, Oronium.
***Thalassothamnidae . Thalassothamnus, Cytocladus. Nomen dubium genus: Conostylus.
** Entactinaria
*** Entactiniidae. Afanasievella, Apophysiactinia, Borisella, Callela, Cancellosphaera, Costaentactinia, Cyclocarpus, Duodecimentactinia, Langsonsphaera, Entactinosphaera, Gracilentactinia, Holdisphaera, Involutentactinia, Kashiwara, Magnentactinia, Magnisphaera, Microporosa, Moskovistella, Multientactinia, Munzuwonella, Paratriposphaera, Perforentactinia, Plenoentactinia, Plenosphaera, Pluristratoentactinia, Polyedroentactinia, Provisocyntra, Radiobisphaera, Retentactinia, Retisphaera, Sinosphaera, Spongentactinia, Stigmosphaerostylus, Trilonche, Uberinterna, Wuyia.
*** Tetrentactiniidae. Multisphaera.
*** Triassothamnidae. Triassothamnus.

Excavates

Malawimonadida

Malawimonadidae. Gefionella, Malawimonas.
Imasidae. Imasa.

Metamonada

The metamonads were first described by Pierre-Paul Grassé in the first volume of Traité de Zoologie, published in 1952, as the superorder Metamonadina or Anaxostylaria. They were originally composed of zooflagellates with four or more flagella, known as polymastigotes and hypermastigotes. These were later split into other groups such as the Parabasalia and Preaxostyla, regarded as individual phyla. After rRNA phylogenetic analyses demonstrated their relatedness, the concept of metamonads was reintroduced by Cavalier-Smith as a monophyletic phylum Metamonada that includes both groups, as well as the anaerobic Fornicata. In this system, Preaxostyla is known as subphylum Anaeromonada, and Fornicata and Parabasalia are two infraphyla that belong to the subphylum Trichozoa. Still, some taxonomists retain the Parabasalia at a phylum level.
The classifications of Preaxostyla and Fornicata were last revised separately in the 2017 Handbook of the protists and the higher classification of Metamonada was revised by Cavalier-Smith in 2021. The classification of Parabasalia was completely updated in 2024. Two new smaller clades of metamonads have been described in addition: anaeramoebae and the 'BaSk' clade, containing barthelonids and skoliomonads. However, Parabasalia was treated as a separate phylum by the 2024 revision, instead of a member of phylum Metamonada. For consistency, the classification listed below maintains Parabasalia as part of the phylum Metamonada.
Phylum Metamonada

Family Anaeramoebidae, genus Anaeramoeba.
'BaSk' clade, genera Barthelona, Skoliomonas.
Subphylum Anaeromonada, class Anaeromonadea
*Order Trimastigida, family Trimastigidae, genus Trimastix.
*Order Paratrimastigida, family Paratrimastigidae, genus Paratrimastix.
*Order Oxymonadida. Genus not assigned to any family: Opisthomitus.
**Family Oxymonadidae, genera Barroella, Oxymonas, Microrhopalodina, Sauromonas, Oxymonites, Microrhopalodites, Sauromonites.
**Family Polymastigidae, genera Blattamonas, Brachymonas, Monocercomonoides, Paranotila, Polymastix, Tubulimonoides.
**Family Pyrsonymphidae, genera Dinenympha, Pyrsonympha, Dinenymphites, Pyrsonymphites.
**Family Saccinobaculidae, genera Notila, Saccinobaculus.
**Family Streblomastigidae, genus Streblomastix.
Subphylum Trichozoa
*Infraphylum Fornicata
**"Carpediemonas-like organisms", genera Aduncisulcus, Carpediemonas, Ergobibamus, Hicanonectes.
***Order Dysnectida, family Dysnectidae, genus Dysnectes.
***Family Kipferliidae, genus Kipferlia.
**Class Eopharyngea
***Family Caviomonadidae, genera Caviomonas*, Iotanema, Euthynema.
***Order Retortamonadida, family Retortamonadidae, genus Retortamonas.
***Order Diplomonadida
****Suborder Distomatina . Enteromonas, Gyromonas*, Hexamita, Spironucleus, Trepomonas, Trigonomonas*, Trimitus.
****Suborder Giardiina . Brugerolleia*, Giardia, Octomitus.
**Order Chilomastigida, family Chilomastigidae, genus Chilomastix.
*Infraphylum Parabasalia. Genera incertae sedis: Chilomitus, Rhizonympha, Tricercomitus, Trichocovina.
**Class Hypotrichomonadea, order Hypotrichomonadida, family Hypotrichomonadidae, genera Hypotrichomonas, Trichomitus.
**Class Pimpavickea, order Pimpavickida, family Pimpavickidae, genera Pimpavicka, Alexandriella.
**Class Trichomonadea
***Order Honigbergiellida
****Family Hexamastigidae, genus Hexamastix.
****Family Honigbergiellidae, genera Honigbergiella, Ditrichomonoides, Honigbergiellopsis, Monotrichomonas.
****Family Cthulhuidae, genera Cthulhu, Cthylla, Nyarlathotep.
****Family Tetratrichomastigidae, genus Tetratrichomastix.
***Order Trichomonadida. Genera incertae sedis: Pseudotrichomonas, Paleotrichomones.
****Family Lacusteriidae, genus Lacusteria.
****Family Trichomonadidae, genera Trichomonas, Cochlosoma, Cyathosoma, Pentatrichomonas, Pentatrichomonoides, Pseudotrypanosoma, Ptychostoma, Tetratrichomonas, Trichomitopsis, Trichomonoides.
**Clade "Tla"
***Class Lophomonadea, order Lophomonadida, family Lophomonadidae, genera Lophomonas, Eulophomonas, Prolophomonas.
***Class Trichonymphea, order Trichonymphida
****Family Burmanymphidae, genus Burmanympha.
****Family Barbulanymphidae, genera Barbulanympha, Rhynchonympha, Urinympha.
****Family Hoplonymphidae, genus Hoplonympha.
****Family Retractinymphidae, genus Retractinympha.
****Family Spirotrichosomidae, genera Spriotrichosoma, Apospironympha, Bispironympha, Colospironympha, Heliconympha, Leptospironympha, Macrospironympha.
****Family Staurojoeninidae, genera Staurojoenina, Idionympha.
****Family Teranymphidae, genera Tetranympha, Eucomonympha, Pseudotrichonympha.
****Family Trichonymphidae, genus Trichonympha.
**Clade "Cadamassta"
***Class Cristamonadea. Genera incertae sedis: Cyclojoenia, Joenia, Joenina, Joenoides, Joenopsis, Pachyjoenia, Parajoenopsis, Placojoenia, Projoenia.
****Order Calonymphida
*****Family Calonymphidae, genera Calonympha, Criconympha, Daimonympha, Diplonympha, Gyronympha, Metastephanonympha, Prosnyderella, Snyderella, Stephanonympha.
*****Family Deltotrichonymphidae, genera Deltotrichonympha, Koruga.
*****Family Mixotrichidae, genus Mixotricha.
****Order Devescovinida, family Devescovinidae, genera Devescovina, Achemon, Astronympha, Bullanympha, Caduceia, Coronympha, Evemonia, Foaina, Hyperdevescovina, Kirbynia, Kofoidia, Macrotrichomonas, Macrotrichomonoides, Metadevescovina, Parajoenia, Polymastigoides, Pseudodevescovina, Runanympha, Devescovites.
****Order Gigantomonadida, family Gigantomonadidae, genus Gigantomonas.
***Class Dientamoebea, order Dientamoebida, family Dientamoebidae, genera Dientamoeba, Histomonas, Parahistomonas, Protrichomonas.
***Class Monocercomonadea, order Monocercomonadida, family Monocercomonadidae, genus Monocercomonas.
***Class Simplicimonadea, order Simplicimonadida, family Simplicimonadidae, genus Simplicimonas.
***Class Tritrichomonadea, order Tritrichomonadida, family Tritrichomonadidae, genus Tritrichomonas.
***Class Spirotrichonymphea
****Order Cononymphida, family Cononymphidae, genus Cononympha.
****Order Holomastigotoidida, family Holomastigotoididae, genera Holomastigotoides, Rostronympha.
****Order Spirotrichonymphida
*****Family Brugerollinidae, genera Brugerollina, Pseudospironympha.
*****Family Fraterculidae, genera Fraterculus, Cuppa.
*****Family Holomastigotidae, genera Holomastigotes, Spiromastigotes, Spirotrichonymphella, Uteronympha.
*****Family Spirotrichonymphidae, genera Spirotrichonympha, Microjoenia, Micromastigotes, Nanospironympha, Spironympha, Torquenympha.

Discoba

Jakobida

Ophirinina
*Agogonidae. Agogonia.
*Ophirinidae. Ophirina.
Andalucina
*Andaluciidae. Andalucia.
*Stygiellidae. Stygiella, Velundella.
Histionina. Histiona, Jakoba, Moramonas, Reclinomonas, Seculamonas nomen nudum.

[Tsukubamonadida]

Tsukubamonadidae. Tsukubamonas.

Heterolobosea

The phylum Heterolobosea contains around 170 species of amoebae, flagellates, and amoeboflagellates. It was initially established to unite two historically well-known amoeboid orders, Schizopyrenida and Acrasida. Later, as more flagellates joined this grouping, the usage of Heterolobosea was split between two meanings: the more common usage applies to the entire clade, while the usage by Cavalier-Smith and collaborators was restricted to a paraphyletic class of "traditional" heteroloboseans, with the name Percolozoa used for the phylum instead. The first comprehensive phylogenomic study of Heterolobosea was published in 2025 by Tomáš Pánek and coauthors, resulting in its modern classification.
Phylum Heterolobosea

Subphylum Pharyngomonada
*Class Pharyngomonadea
**Order Pharyngomonadida
***Family Pharyngomonadidae, genus Pharyngomonas.
Subphylum Tetramitia
*Multisulcus malaysiensis
*Family Orodruinidae, genera Gruberella, Orodruina, Stachyamoeba.
*Class Selenaionea
**Order Neovahlkampfiida
***Family Neovahlkampfiidae, genus Neovahlkampfia.
**Order Selenaionida
***Family Selenaionidae, genus Selenaion.
*Class Eutetramitea. Genera not assigned to any order and family: Euplaesiobystra, Fumarolamoeba, Heteramoeba, Parafumarolamoeba, Paravahlkampfia, Oramoeba, Vrihiamoeba.
**Order Naegleriida . Genera not assigned to any family: Aurem, Marinamoeba.
***Family Acrasidae, genera Acrasis, Allovahlkampfia, Pocheina.
***Family Naegleriidae, genera Naegleria, Willaertia, Trimastigamoeba*.
***Family Tulamoebidae, genera Pleurostomum, Tulamoeba.
***Family Vahlkampfiidae, genera Tetramitus, Vahlkampfia, Pseudovahlkampfia*, Tetramastigamoeba*.
**Order Percolomonadida
***Family Barbeliidae, genera Barbelia, Nonamonas.
***Family Lulaidae, genus Lula.
***Family Percolomonadidae, genus Percolomonas.
**Order Pseudociliatida
***Family Stephanopogonidae, genus Stephanopogon.
**Order Creneida
***Family Creneidae, genus Creneis.
**Order Lyromonadida
***Family Psalteriomonadidae, genera Harpagon, Psalteriomonas, Monopylocystis, Pseudoharpagon, Sawyeria, Lyromonas.

Euglenozoa

The phylum Euglenozoa is home to at least 2,000 described species of single-celled flagellates of very dissimilar lifestyles. It was originally proposed to group the euglenids and the kinetoplastids, usually studied separatedly; eventually it included diplonemids and symbiontids as well. Due to its share of photosynthetic species, traditionally regarded as algae, the phylum is also known as Euglenophyta by phycologists, and euglenids in particular were often studied as algae. Euglenids and kinetoplastids are the most diverse in terms of described species, although diplonemids may compose over 67,000 potential species. The classification of euglenozoans was summarized by Cavalier-Smith in 2016. A more phylogenetically precise revision of their classification was published in 2021 by Alexei Kostygov and coauthors, with newer clades and genera described in the following years, particularly of euglenids. Still, one group of euglenids, the paraphyletic "ploeotids", remains unresolved in the current classification, spread out across multiple clades.
Phylum Euglenozoa

Class Euglenida . Genera not assigned to any lower clade: Moyeria, Entosiphon, Gaulosia. Genera incertae sedis: Atraktomonas*, Calycimonas*, Dolium*, Dylakosoma*, Tropidoscyphus*, Michajlowastasia*, Parastasiella*, Dinemula*, Paradinemula*, Mononema*, Ovicola*, Embryocola*, Copromonas*.
*Order Petalomonadida, genera Biundula, Notosolenus, Pentamonas*, Petalomonas, Scytomonas, Sphenomonas.
* Alistosa, genera Ploeotia, Serpenomonas, Keelungia, Lentomonas, Decastava.
* Karavia, genera Hemiolia, Liburna.
* Olkaspira. Genera not assigned to any lower clade: Chelandium, Olkasia.
** Spirocuta
***Anisonemia
****Order Anisonemida, family Anisonemidae, genera Anisonema, Dinema, Heteronema.
****Order Natomonadida
*****Family Neometanemidae, genus Neometanema.
***** Aphagea
******Family Astasiidae, genera Astasia, Gyropaigne, Menoidium, Parmidium, Rhabdomonas.
******Family Distigmidae, genus Distigma.
***Order Peranemida, family Peranemidae, genera Chasmostoma, Jenningsia, Peranema, Teloprocta, Urceolus.
***Euglenophyceae . Genera incertae sedis: Ascoglena*, Euglenamorpha*, Euglenopsis*, Glenoclosterium*, Hegneria*, Klebsina*, Euglenocapsa*.
****Order Rapazida, family Rapazidae, genus Rapaza.
****Order Eutreptiales, family Eutreptiaceae, genera Eutreptia, Eutreptiella.
****Order Euglenales
*****Family Phacaceae, genera Discoplastis, Flexiglena, Lepocinclis, Phacus.
*****Family Euglenaceae, genera Colacium, Cryptoglena, Euglena, Euglenaformis, Euglenaria, Monomorphina, Strombomonas, Trachelomonas.
Class Symbiontida, genera Bihospites, Calkinsia, Postgaardi.
Class Diplonemea, order Diplonemida
*Family Diplonemidae, genera Diplonema, Rhynchopus, Lacrimia, Sulcionema, Flectonema.
*Family Hemistasiidae, genera Hemistasia, Namystinia, Artemidia.
*Family Eupelagonemidae, genus Eupelagonema.
Class Kinetoplastea. Genera incertae sedis: Bordnamonas*, Cephalothamnium*, Desmomonas*, Jarrellia*, Lamellasoma*.
*Subclass Prokinetoplastia, order Prokinetoplastida
**Family Ichthyobodonidae, genus Ichthyobodo.
**Family Perkinselidae, genus Perkinsela.
*Subclass Metakinetoplastia
**Family Allobodonidae, genera Allobodo, Novijibodo.
**Order Neobodonida
***Family Neobodonidae, genera Actuariola, Avlakibodo, Azumiobodo, Cruzella, Cryptaulaxella, Klosteria, Neobodo, Phanerobia, Rhynchobodo.
***Family Rhynchomonadidae, genera Dimastigella, Rhynchomonas.
**Order Parabodonida
***Family Cryptobiidae, genera Cryptobia, Parabodo.
***Family Trypanoplasmatidae, genera Procryptobia, Trypanoplasma.
**Order Eubodonida, family Bodonidae, genus Bodo.
**Order Trypanosomatida, family Trypanosomatidae. Genera not assigned to subfamilies: Jaenimonas, Vickermania, Sergeia, Wallacemonas. Genera incertae sedis: Cercoplasma, Malacozoomonas, Nematodomonas, Rhynchoidomonas, Paleoleishmania.
***Subfamily Trypanosomatinae, genus Trypanosoma.
***Subfamily Leishmaniinae
****Infrafamily Crithidiatae, genera Leptomonas, Crithidia, Lotmaria.
****Infrafamily Leishmaniatae, genera Leishmania, Porcisia, Endotrypanum, Novymonas ''Zelonia, Borovskyia.
***Subfamily Herpetomonadinae, genera Herpetomonas, Lafontella, Phytomonas.
***Subfamily Strigomonadinae, genera Angomonas, Strigomonas, Kentomonas.
***Subfamily Blastocrithidiinae, genera Blastocrithidia, Obscuromonas.
***Subfamily Blechomonadinae, genus Blechomonas.
***Subfamily Paratrypanosomatinae, genus Paratrypanosoma''.

Minor clades

''Meteora sporadica''

Ancyromonadida

Divimonas

Ancyromonadidae. Ancyromonas, Nutomonas.
Planomonadidae. Fabomonas, Planomonas.

Telonemia

The phylum Telonemia contains a few species of flagellates found in ocean and fresh waters worldwide. It was originally proposed in 2006 for Telonema, a genus of previously uncertain affinity. Under the Cavalier-Smith system, telonemids were initially classified as a class of Cryptista, but later analyses consistently recovered it as a separate group. Until 2019, only two species had been formally described, each belonging to a separate genus, but environmental DNA sequencing suggested there were many more species not yet described. Between 2022 and 2025, eight additional species were described along with three new genera, bringing the total number of species to ten.
Phylum Telonemia, class Telonemea, order Telonemida, family Telonemidae, genera Arpakorses, Lateronema, Hyaloria, Microkorses, Telonema.

Protists of uncertain affiliation

Acinetactis, Actinastrum, Actinocoma, Actinolophus, Adinomonas, Aletium, Amphimonas, Amylophagus, Aphelidiopsis, Asterocaelum, Asthmatos, Aurospora, Barbetia, Berkeleyaesol, Belaria, Belonocystis, Bertarellia, Bertramia, Bodopsis, Boekelovia, Branchipocola, Camptoptyche, Chalarodora, Cibdelia, Cichkovia, Cinetidomyxa, Cingula, Cladomonas, Clathrella, Codonoeca, Coelosporidium, Copromonas, Cyanomastix, Cyclomonas, Cytamoeba, Dallingeria, Dictyomyxa, Dimastigamoeba, Dinemula, Dinoasteromonas, Diplocalium, Diplomita, Diplophysalis, Diploselmis, Dobellina, Ducelleria, Ectobiella, Elaeorhanis, Embryocola, Endamoeba, Endemosarca, Endobiella, Endomonas, Endospora, Enteromyxa, Eperythrocytozoon, Errera, Fromentella, Gweamonas, Gymnococcus, Gymnophrydium, Haematotractidium, Hartmannina, Heliobodo, Heliomonas, Hermisenella, Heterogromia, Hillea, Hyalodaktylethra, Immanoplasma, Isoselmis, Janickina, Kamera, Labyrinthomyxa, Lagenidiopsis, Liegeosia, Luffisphaera, Lymphocytozoon, Lymphosporidium, Macappella, Magosphaera, Malpighiella, Martineziella, Megamoebomyxa, Microcometes, Monochrysis, Monodus, Mononema, Myrmicisporidium, Naupliicola, Nephrodinium, Neurosporidium, Orbulinella, Ovicola, Palisporomonas, Pansporella, Paradinemula, Parakaryon, Paraluffisphaera, Paramonas, Paraplasma, Parastasia, Parastasiella, Peliainia, Peltomonas, Petasaria, Phagodinium, Phanerobia, Phloxamoeba, Phyllomitus, Phyllomonas, Physcosporidium, Pleuophrys, Pleuromastix, Protenterospora, Protomonas, Pseudoactiniscus, Pseudosporopsis, Rhizomonas, Rhynchodinium, Rigidomastix, Schewiakoffia, Sergentella, Serpentoplasma, Sphaerasuctans, Spongastericus, Spongocyclia, Stephanomonas, Strobilomonas, Tetradimorpha, Thaulirens, Topsentella, Toshiba, Trichonema, Urbanella.