Macquaria is an endemic freshwater fish genus that is of importance to Australian fisheries management. Macquaria ambigua is widely distributed across central and eastern Australia (Murray-Darling, Lake Eyre, Bulloo and Fitzroy basins) and is a prized recreational fishing species that has been stocked throughout most of its range. On the other hand, Macquaria australasica has a restricted distribution in eastern Australia (Murray-Darling, and some south eastern NSW coastal basins), is classified as vulnerable in New South Wales and stocking activity has been limited. This project aims to elucidate the historical patterns of population genetic structure and diversification in both species. It will identify distinct evolutionary units, and assess the effect of fish stocking on the genetic diversity and structure of populations. In order to achieve these aims a comprehensive collection of samples has been obtained from across each species range. Mitochondrial DNA (mtDNA) sequence data has been used to reconstruct the genealogical history of both species based on coalescence methods, the results of which will be presented here. This research has important implications for the management of M. ambigua and M. australasica, and fisheries management in general.