Many Murray-Darling Basin (MDB) freshwater fishes have experienced extreme declines, with around a quarter of the freshwater fishes threatened with extinction. Here we target three native fishes that were once widespread across the MDB, but today have all had significant declines (Purple Spotted Gudgeon, Olive Perchlet and Darling Hardyhead). Remnant populations are extremely geographically limited, with some recently discovered populations occurring outside of the perceived natural range of the species. Existing genetic data have been unable to clarify whether these populations are endemic or translocated. Recovery actions for remnant populations are consequently very difficult to prioritise. We are now applying genetic data from thousands of loci from next generation double digest RAD sequencing, coupled with comprehensive sampling from all potential source populations. Together this should unequivocally distinguish the native status of each population. It will also provide key information regarding each populations genetic diversity, divergence between populations and whether any loci appear to be related to potential local adaptations. These results can then be used to guide reintroduction efforts and conservation strategies.