Abstract – Releases of non-native trout often result in introgression into natural populations and negative genetic effects. The causal ecological mechanisms for a wide range of reported outcomes are poorly understood. Brown trout population structure in an alpine lake with three major recruitment streams was assessed by analysis for eight DNA microsatellite markers and compared with the non-native population. The lake is subject to a 40-year recorded history of stocking with exogenous trout. No certain deviations from Hardy–Weinberg equilibrium were found. Tests for population differentiation and genetic distance indicated separate populations for all the sampled areas, and with the exogenous population as a cluster quite different from the others. Assignment tests indicated that only a small fraction of the fish sampled from the lake originated from the introduced trout strain (<3%). Wild discriminate, naturally reproducing populations characterize this alpine lake ecosystem, in spite of 40 years of stocking, which appears to have had a limited impact. It is unlikely that this population structure can ultimately be explained by trout movement patterns. Genetic analysis needs to be supplemented by studies of local life history strategies, to evaluate the relative importance of local adaptation versus random genetic differentiation, because implications for conservation and management are different.