When first described, the Monito gecko was thought to be closely related to either the Mona dwarf gecko (Sphaerodactylus monensis), an endemic of the island of Mona located approximately 5 km southeast of Monito or to the Desecheo dwarf gecko (Sphaerodactylus levinsi) an endemic of the island of Desecheo. Subsequent studies proved that the Monito gecko is more closely related to S. macrolepis, a species common throughout the Puerto Rican Bank.