Large scale harvesting and other anthropogenic activities have caused severe population declines in many commercially important fish populations, but accurate information about census and effective population size is often hard to come by. Available evidence suggests that in marine fishes, effective population size (N(e)) is often several orders of magnitude smaller than census size, such that intensively harvested populations may be particularly vulnerable to loss of genetic diversity. The European whitefish (Coregonus lavaretus) has a long history of heavy exploitation in the Baltic Sea, and the Finnish commercial catch of the species has been substantially reduced, despite high fishing effort. We investigated the temporal genetic stability of migratory whitefish populations from two Finnish rivers (Tornionjoki and Kiiminkijoki), sampled at least twice between 1981 and 2006, by assaying variability in 21 microsatellite loci. Our results suggest a small, albeit significant (F(ST) = 0.004; p = 0.008) and temporally stable, degree of differentiation between rivers. However, in contrast to earlier reports, heterochronous runs (ascending groups) from Tornionjoki did not exhibit significant genetic divergence. Bayesian estimates of N(e) suggest substantial declines from historic levels dating to ca 250 years. Yet despite a probable decrease in census population size over the study period, we detected no significant change in contemporary N(e). Within group genetic diversity appeared largely unchanged over this time frame; however, we detected a trend towards decreased differentiation between spawning groups (rivers) since the 1980s. These results are discussed in light of stocking programs and conservation of genetic diversity of natural populations.