Abstract – Local genetic differentiation may potentially arise in recently fragmented populations. Brown trout is a polytypic species exhibiting substantial genetic differentiation, which may evolve in few generations. Movement (semi-)barriers in rivers may cause fragmentation, isolation and genetic differentiation in fish. In the Måna River (28 km) flowing from the alpine Lake Møsvatn to the boreal Lake Tinnsjø, construction of four hydropower dams during the period 1906–1957 have fragmented the previously (since last Ice Age) continuous wild resident brown trout population. Samples from the two lakes (N = 40) and six sites in the river (N = 30) isolated at different times were analysed at nine microsatellite loci. All populations showed substantial genetic variation (mean number of alleles per locus 5.3–8.9, observed heterozygosity 0.57–0.65 per population, overall Fst = 0.032). Pairwise multilocus Fst estimates indicated no significant differentiation between populations in the two lakes, and no or little differentiation in the lower river (Fst = 0.0035–0.0091). The microgeographic differentiation among wild resident trout at these sites was less than expected based on similar previous studies. However, results from the upper river, in particular the site immediately below the Lake Møsvatn outlet and dam, indicated isolation (Fst > 0.035). Calculation of genetic distances and assignment tests corroborated these results, as did a significant correlation between years of isolation (since dam construction) and Fst. The population structuring is most likely a result of fragmentation by dams, which has increased overall genetic diversity. This increased local differentiation may be caused by natural selection, but more likely by genetic drift in small, recently fragmented populations. Increased local genetic diversity by genetic drift does not justify conservation measures aiming at preserving genetic diversity.