Identifying species and the relationships among them remains important for assessing biodiversity trends and is a critical focus for reversing global biodiversity loss. The saw-shelled turtles of Australia, in the genus Myuchelys, show cryptic diversity and include species that range from Endangered (M. bellii), through those that are locally abundant but extremely limited in distribution (M. georgesi and M. purvisi) to those that are common and widespread (M. latisternum). The Endangered M. bellii is restricted to 3 small isolated populations in the headwaters of the Murray-Darling basin, in the Border, Gwydir and Namoi tributaries. There is no evidence of strong differentiation among these 3 populations based on mitochondrial DNA (mtDNA) divergences; rather there is only a shallow genetic structure ranging from 0.1 to 0.3% divergence. The 3 restricted and small populations of the Endangered M. bellii face a number of threatening processes and require conservation management across state boundaries as a single biological species. The mtDNA phylogeny supports previous phylogenetic findings of a deep hylogenetic divergence between M. purvisi and M. georgesi (13.5% mtDNA) and the sister taxa relationship of M. latisternum and M. bellii. A notable exception was our finding that Emydura macquarii and M. georgesi are sister taxa inside the Myuchelys radiation.