Microstigmata amatola is endemic to South Africa, with a very restricted distribution in the Eastern Cape province. The species is known from only two collection localities approximately 35 km apart: Hogsback in the Amatola Mountains and Stutterheim Kologha Forest.
The species is a ground-dwelling wandering spider that appears to be restricted to conditions of high humidity and relatively even temperature as found in the understory and litterlayer of indigenous forest and close-canopy bush. It has been sampled from the Forestbiome at altitudes ranging from 1,052 to 1,372 m above sea level.
Microstigmata amatola was described by Charles Griswold in 1985 from specimens collected at Hogsback in the Amatola Mountains. The species is known from both sexes and belongs to the genusMicrostigmata, which is the only representative of the family Microstigmatidae in South Africa.