During the Miocene, central and western Australia shared a warm–wet environment that harboured a mesic rainforest fauna. Now, although the area is within the arid climate zone, it provides a habitat for highly diverse groundwater-associated invertebrates. Periods of global cooling and aridification during the late Miocene resulted in isolated desert refuges that retained ancient lineages. We aimed to characterise oniscidean isopod crustaceans from three refugial locations in the arid zone, and salt lakes, to identify new putative species. Extensive sampling and sequencing of the mitochondrial Cytochrome Oxidase c subunit 1 gene and the 18S rRNA gene were conducted. A molecular phylogenetic analysis of the oniscidean genus Haloniscus showed results consistent with a relictualisation hypothesis of widespread populations from across South Australia to Western Australia with subsequent geographic isolation and diversification of new species within habitats. We observed significant regional endemicity, but some lineages were not regionally monophyletic, pointing to past connectivity. We expand the range of Haloniscus and identify at least 26 putative species from arid-zone locations in Australia, with substantial phylogeographic structure within locations. These findings highlight the importance of relictual groundwater habitats as refugia for a diverse fauna representing early climatic history in Australia’s arid zone.