1. Introgression into natural salmonid populations from stocked conspecifics has been widely studied. Outcomes vary from no effect even after decades of stocking, to population replacement after only a couple of generations. Potential introgression caused by semi-supportive breeding (i.e. using a mixture of local strains as brood stock) is, however, less well studied.
2. We investigated population structure of brown trout (Salmo trutta) in a regulated alpine lake with three natural, environmentally contrasting tributaries used as spawning and rearing habitat. Massive semi-supportive breeding of admixed local strains has been implemented for decades. Stocked trout represented c. 17% of the total lake population, and a substantial post-release survival reflects a considerable potential for introgression. However, the mark-recapture studies indicate no spawning runs of stocked fish.
3. Using 13 polymorphic microsatellite loci, we found natural straying and non-native reproduction, especially among wild populations inhabiting environmentally unstable habitat. Retained genetic structure across tributaries indicated low reproductive success of wild-born non-natives. Moreover, the genetic structure among tributaries has probably not been influenced by semi-supportive breeding, because of recruitment failure of stocked trout.