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The Australian stygofauna comprises a unique and diverse assemblage of invertebrates, of which the amphipod crustaceans are a dominant but poorly described element. Recent exploration of the Western Australian stygofauna, in particular the Yilgarn region of central Western Australia, has shown evidence of great species diversity, with numerous individual calcrete aquifers found to contain unique assemblages of invertebrate species. A recent fine-scale biodiversity initiative, using COI barcoding, of a single calcrete aquifer (Sturt Meadows) in the Yilgarn region reported the presence of three divergent and morphologically cryptic stygobitic lineages of amphipods from Chiltoniidae, which represent undescribed taxa. This paper details the subsequent systematic analysis of these COI lineages and presents a broader phylogeny and detailed morphological analyses of the lineages. The report of cryptic species was not supported upon morphological examination and three new species from three new genera (Scutachiltonia n. gen., Stygochiltonia n. gen., and Yilgarniella n. gen.) are described from the Sturt Meadows calcrete aquifer. The three genera do not form a monophyletic group and are instead believed to have evolved from separate colonisation events from distinct ancestors rather than from speciation events within the aquifer. This work contributes to a broader research initiative, documenting the presence of a rich subterranean invertebrate fauna in the Yilgarn region.