Genetic variability and population structure of Baltic ringed seals and an Arctic reference population were assessed using eight microsatellite loci. Ringed seals colonized the Baltic Sea basin soon after deglaciation 11 500 years ago and are supposed to have remained largely isolated from the main Arctic stock since then, ≈1000 generations. In the 1900s the Baltic population declined rapidly, and is now confined to three distinct breeding areas, with N < 6000 seals altogether. Microsatellite heterozygosity in ringed seals was higher than that in the closely related, boreal harbour seal and grey seal, for which the markers were initially developed. This is plausibly attributed to an overall greater population (species) size of ringed seals during the Quaternary. Allele frequency differentiation between the Baltic and Arctic ringed seals, conventionally treated as different subspecies, was weak. Assuming complete isolation, the divergence (FST=0.023) would imply a notably high postglacial effective population size, ≈20 000 for the Baltic population. The isolation assumption however, seems unrealistic in the light of the data: a coalescent-based simulation approach to the likelihood of alternative demographic histories clearly favoured a scenario with recurrent gene flow to the Baltic, over one of complete isolation (drift only). Within the Baltic Sea, no differentiation was found between the Gulf of Finland and the Gulf of Bothnia breeding areas; the recent population decline and split have not yet affected the inbreeding levels of the disjunct breeding stocks.