The majority of Australian Spinicaudata Linder, 1945 inhabit the (semi)arid deserts of Australia’s lowlands. However, several closely related species of Paralimnadia Sars, 1896 inhabit small temporary habitats throughout the Great Dividing Range in eastern Australia. By combining analyses of mitochondrial cytochrome c oxidase subunit I (COI) with double-digest restriction-site associated DNA (ddRAD) data, we studied the species diversity and genetic diversity of this group of mountain-dwelling branchiopods. Levels of genetic differentiation in COI are relatively low between putative species (mostly between 1.5 and 6.7%), complicating COI-based species delimitation. Depending on the applied threshold, three to six species are inferred in the studied area, with most putative species being geographically restricted. Particularly notable are the high levels of population differentiation indicated by ddRAD analyses between nearby populations within putative species. This suggests that gene flow is limited, even between populations separated only by a few kilometres. This may lead to fast population differentiation, which in turn might drive speciation. Our data suggest that the species diversity of Paralimnadia in the Great Dividing Range is much higher than currently appreciated.