Rivers in north-western Australia have been long isolated systems and several of them, including those in the central north Kimberley (CNK) and Pilbara (PIL) regions, are known for their endemism in freshwater fishes. Furthermore, some species of freshwater fish are shared between rivers of the south-western Kimberley (SWK) and rivers of the western Arafura-Carpentarian (WAC) regions to the exclusion of CNK, despite CNK being geographically intermediate to these regions. This suggests that the freshwater biota of the CNK may have an independent evolutionary history with respect to the SWK and the WAC, and that the latter two may have relatively strong biogeographic affinities. This pattern warrants further examination using phylogeographic analyses of freshwater biota, such as freshwater caridean shrimp. In this study we used mtDNA data and conservation biogeographic approaches to assess molecular patterns of biodiversity within freshwater shrimp, genus Caridina (Atyidae), in north-western Australia using reported biogeographic patterns in freshwater fishes as a hypothesis. Specifically, we expected CNK and PIL to have higher endemism and phylogenetic diversity (PD) within Caridina than SWK and WAC, and shrimps of SWK and WAC to have stronger biogeographic affinities with one another than either one has with CNK. Results showed high endemism within genus Caridina from the CNK and PIL, although PD and species richness was lowest for PIL and highest for CNK. Two lineages within Caridina were shared between the SWK and the WAC to the exclusion of the CNK. The results of this study for Caridina shrimp are thus strikingly similar to previous analyses of freshwater fishes, and support earlier studies that define PIL as a bioregion. We suggest that the incorporation of phylogeographic data for both fishes and freshwater macroinvertebrates (i.e. shrimps and molluscs) in future analyses may also identify CNK as a bioregion.