Fish stocking is an important tool in aiding the recovery of native fish populations in the Murray–Darling Basin (MDB) where millions of fish are stocked annually. Until now, it has been difficult to detect stocked fish in the MDB and to determine their hatchery of origin. FishGen is a multi-institutional program that uses non-destructive genetic parentage and kinship testing to differentiate between stocked and wild fish of multiple species, including Murray cod, golden perch and silver perch. Data analyses include matching wild-caught fish to a reference database of hatchery broodstock. To date, 4,776 fish (2,171 broodstock and 2,605 wild-caught) have been analysed. FishGen has informed hatcheries on the genetic relatedness and inbreeding of their broodstock, so hatcheries can select appropriate individuals for breeding and remove inbred fish from their programs. These actions maximise the genetic diversity and health of stocked fish. Approximately 5% of the wild-caught fish were shown to be stocked in origin, a number that will likely increase with the recent collection of 800 broodfish samples. The project is the largest of its kind in Australia and demonstrates the benefits of a well-managed collaborative genetic program to improve the genetic health of wild fish populations.