Three new freshwater ameirid species were discovered in the Western Australian subterranean habitats and described in this paper. They all proved to belong to the genus Nitocrellopsis Galassi, De Laurentiis & Dole-Olivier, 1999, representing the first record of this genus in Australia. Nitocrellopsis operculata sp. nov. was collected in 2003 in the Pilbara region, during the Pilbara Regional Survey, led by the Western Australian Department of Environment and Conservation (DEC). It can be distinguished from all other congeners by the reduced armature of the antennal exopod, which is an autapomorphic feature. Also, no other species of Nitocrellopsis has cuticular windows on prosomal or urosomal somites, or six elements on the third exopodal segment of the second leg. Nitocrellopsis halsei sp. nov. and N. pinderi sp. nov. are sister-species, collected in 2007 in the neighbouring Yilgarn region, by the private environmental consulting company Bennelongia Pty Ltd. Numerous morphological similarities include somite ornamentation, armature patterns of the swimming legs and the fifth leg, as well as the shape and armature of the antennula, antenna and almost all mouth appendages, while the main differences between the two are observed in the body size and habitus appearance, caudal rami shape and size, presence/absence of large lateral pores on the fourth pedigerous somite, number of spinules on the anal operculum, number of setae on the madibular endopod, and shape of the exopod of the fifth leg. Although they differ from any other congener by a combination of characters, no significant autapomorphic features were observed. In order to find a more natural allocation of these three species, a cladistic analysis is performed on all current members of Nitocrellopsis and three outgroup taxa, based on 45 morphological characters. The resulting cladogram shows that the ingroup is well defined by at least four synapomorphies, but the Australian species from the two regions are only remotely related to each other, showing the importance of looking at small-scale patterns when inferring Gondwanan biogeography. Three sister-species pairs are recognized in the genus and a key to all 12 members is provided.