Abstract To preserve the local genetic patrimony of wild aquatic species, population enhancement should be limited to supportive breeding of native lineages and controlled releases in target areas with depleted population size. This is the case of brown trout, Salmo trutta L., in northern Iberia, a species of high economic and cultural value in the region. Employing a combination of conserved and hypervariable genetic markers, illegal stocking of domestic brown trout in protected areas (National Park, Natural Reserve) within the Cantabric chain was detected. The most likely origin of the domestic individuals was determined by assignment tests to hatchery stocks as a result of past releases conducted downstream and out of the protected areas. Where connectivity exists along a water course, the entire drainage should be considered as a single management unit to preserve the native genetic diversity of upstream protected areas.