Abstract Murray cod, Maccullochella peelii (Mitchell) is an iconic Australian species endemic to the Murray-Darling Basin (MDB) of inland south-eastern Australia. Murray cod has been a valuable food source and supported a large commercial fishery throughout much of the 20th century. Over-fishing and habitat destruction have resulted in significant declines in Murray cod populations throughout much of its range. Since the early 1980s, large numbers of Murray cod have been stocked into waterways to support both recreational fishing and conservation efforts. In this study, the likely impacts of past and current stocking practices on genetic diversity of Murray cod were modelled and new strategies to maximise genetic diversity in stocked populations are explored. The results suggest that a large, well-managed breeding and stocking programme could help maintain genetic diversity of Murray cod across the MDB. In catchments within the MDB where the effective population size is very small, a well-designed stocking programme, following strict guidelines for numbers of families reared and number of individuals maintained per family, could increase genetic diversity in a few generations.