Based on estimates of genetic differentiation between populations, assignment tests and analysis of isolation by distance, stocked populations of brown trout Salmo trutta of Funen Island, Denmark, had been genetically affected by domesticated trout, whereas the stocking of wild exogenous trout into one of the rivers had little or no impact. At the same time, there were clear indications of remaining indigenous gene pools in the Funen populations. The management implications of these findings are discussed and changes in trout release activity are recommended to avoid further mixing of trout gene pools.