Cherax is a genus of 58 species of decapod crustaceans that are widespread across Australia and New Guinea. We use single-nucleotide polymorphisms (SNPs) to examine phylogeographic patterns in the most widespread species of Cherax, namely, C. destructor, and test the distinctiveness of one undescribed species, two C. destructor subspecies, previously proposed evolutionarily significant units, and management units. Both the phylogenetic analyses and the analysis of fixed allelic differences between populations support the current species-level taxonomy of C. setosus, C. depressus, C. dispar and C. destructor, the distinctiveness of C. destructor albidus and C. d. destructor and the existence of one undescribed species. The two populations of C. d. albidus from the Glenelg and Wimmera rivers were significantly distinct, with eight diagnostic differences (<1% fixed differences, null expectation is four fixed differences), but this low level of divergence is interpreted as within the range that might be expected of management units, that is, among allopatric populations of a single species or subspecies. A southern clade of C. d. destructor comprising the Murray River and its tributaries upstream from its confluence with the Darling River is genetically distinct from a northern clade comprising populations from the Lake Eyre Basin, the northern half of the Murray–Darling Basin (Darling River catchment) and the Lower Murray River below the Darling confluence.