The long-term genetic consequences of supportive breeding programs are not well understood. Nevertheless, stocking populations with hatchery-produced fish to compensate for losses of natural production are common practice, for example after constructions of hydroelectric power dams. Hatcheries typically fertilize eggs using ‘mixed-milt fertilizations’, without consideration to natural reproductive behaviours, and hence, natural selective regimes would be altered. Here, a series of experiments with focus on Mhc and mate choice in a population of brown trout (Salmo trutta L.) with a history of long-term stocking are presented. The major histocompatibility complex (Mhc) constitutes of genes coding for antigen presentation in the vertebrate immune system. In addition to the immunological function, Mhc genes might also influence reproductive behaviours such as mate choice. For example, in some species individuals are able to recognize Mhc genotypes of potential mates and to some extent base their mate choice on this information. Here, I address these questions on brown trout. Can the phenomena be observed in brown trout? Could such mechanisms help individuals to avoid inbreeding, or are other mechanisms important? How does the artificial rearing of fish for enhancement of natural populations relate to these issues? The results presented here, in combination with previous work, shows that several factors are important in the process of pair formation in salmonid species. For example, females of the studied population used more than a single criterion when choosing among the available mates Mhc genes and males with certain Mhc genotypes achieved more matings, possibly an effect from increased fighting ability. Further, the population appears to contain an unnatural high level of Mhc variation, and some results indicate that the population might suffer from outbreeding depression at the Mhc. These negative effects are most likely derived from compression of sub-populations after dam-construction, in combination with supportive breeding with no consideration to natural spawning behaviour.