This species, initially described as such by Townsend in 1912, was listed as a subspecies of Neotoma lepida by Burt in 1932. Patton et al. revised the systematic position of Neotoma lepida and found it to be a species complex, with N. l. insularis being readily distinct from N. lepida, by means of mtDNA phylogeny and various morphological attributes, therefore reverting this population to its initial status as a species, as described by Townsend.