Abstract – We studied the effect of stocking brown trout in three alpine lakes (Skavatn, Midtre Grøndalsvatn and Nordmannslågen) of the Hardangervidda mountain plateau by comparing microsatellite data from historical (1933 and 1967) and contemporary (2003) population samples. Historical and contemporary samples from a control lake (Krokavatn) and a contemporary sample from Gjuvsjå (suspected donor lake) were included as well. A total of 331 brown trout were genotyped with 11 microsatellites. Very low level of genetic diversity is observed in the historical samples from Nordmannslågen and Midtre Grøndalsvatn but not in the contemporary samples. In Skavatn historical and contemporary samples show similar genetic diversity as in the other contemporary samples. Admixture analyses with the structure program indicate high levels of introgression by nonnative brown trout in all three lakes. The stocking source for two lakes (i.e. from Gjuvsjå) is partially verifiable via our analyses. The high introgression in these lakes is discussed and the management issues are briefly addressed.