To elucidate the colonization of freshwater fish into Norway following the last deglaciation of Europe 10,000 years ago, we have performed a survey using mitochondrial DNA variation (20 populations) and multilocus DNA fingerprinting (14 populations) of the widely distributed perch (Perca fluviatilis) from the Scandinavian peninsula and the Baltic Sea. Sequence analysis of a 378 bp segment of the perch mitochondrial control region (D-loop) revealed 12 different haplotypes. A nested clade analysis was performed with the aim of separating population structure and population history. This analysis revealed strong geographical structuring of the Scandinavian perch populations. In addition, the level of genetic diversity was shown to differ considerably among the various populations as measured by the bandsharing values (S-values) obtained from multilocus DNA fingerprinting, with intrapopulation S-values ranging from 0.19 in Sweden to 0.84 in the central part of Norway. Analysis of the intrapopulation S-values, with S-value as a function of lake surface area and region, showed that these differences were significant. The mitochondrial and DNA fingerprinting data both suggest that the perch colonized Norway via two routes: one from the south following the retreating glacier, and the other through Swedish river systems from the Baltic Sea area. Perch utilizing the southern route colonized the area surrounding Oslofjord and the lakes which shortly after deglaciation were close to the sea. Fish migrating from the Baltic Sea seem to have reached no further than the east side of Oslofjord, where they presumably mixed with perch which had entered via the southern route. It seems likely that the migration events leading to the current distribution of perch also apply to other species of freshwater fish showing a similar distribution pattern.