There is a long tradition of artificially stocking lakes and rivers with fish in the hope to increase the quality and amount of fish that can be harvested. The animals used for stocking often originate in distant hatcheries or hatcheries that breed fish from remote regions. This stocking practice could have effects on the genetic integrity of resident populations. We have analysed here a case of the influence of stocking on Alpine populations of the Arctic charr (usually included into Salvelinus alpinus, but revised to Salvelinus umblaKottelat 1997) within a unique geographical and historical setting. The Königssee in the Bavarian Alps (Berchtesgaden) was heavily stocked several times during the last century. However, a sample of the ancestral Königssee population still exists in the Grünsee, which lies close to Königssee, but 1000 m higher. To trace the influence of stocking in Königssee we have analysed more than 300 individuals from 10 lake populations, including the source populations of the fish used for stocking. From these we have sequenced a part of the mitochodrial control region and have typed them at six microsatellite loci. The differential distribution of haplotypes, as well as assignment tests, show that the influence of stocking on the genetic integrity of the Königssee population has been negligible. However, our data reveal that in another lake included in our study (Starnberger See), the ancestral population was apparently replaced completely by the populations used for stocking. The major difference between the lakes is the relative preservation of ecological integrity. Königssee was ecologically stable in the past, whereas Starnberger See was heavily polluted at one point, with charr approaching extinction. Interestingly, in a lake neighbouring Starnberger See, the Ammersee, which was also subject to strong pollution but not stocked, the ancestral population has recovered. Our data suggest that the practice of artificial stocking should be reconsidered, or at least monitored for effectiveness.