Golden perch (Macquaria ambigua) and Murray cod (Maccullochella peelii) are two Australian native freshwater fish species widely distributed in the Murray Darling basin. Both of them are important angling fish but wild populations have been declining for the last few decades due in part to altered hydrologic regimes and construction of dams and weirs. Measures in the Murray Darling basin to conserve these species include widespread stocking of rivers from hatchery raised fish. The Lachlan river has a very dynamic flow regime due to altered hydrology, and large numbers of hatchery raised golden perch and Murray cod have been released into the river every year since 1984. It is now unclear whether a wild breeding population of these two species still occurs in the Lachlan river or whether the current population is maintained by stocking. In this study, we performed a genetic analysis of golden perch and Murray cod including population genetic structure and the contribution of stocking to populations in the Lachlan river. Our analysis suggests a low level of genetic diversity and limited evidence of breeding activity of golden perch in the catchment. Furthermore, genetic data of Murray cod form different sections of Lachlan catchment also showed limited structuring and marginal variation within individual from the catchment and between Lachlan and hatchery sourced fish. Based on the outcome of genetic analysis we are currently examining otolith microchemistry to evaluate natal origins of stocked fish.