The pelagic and gregarious, low Arctic harp seal (Phoca groenlandica) is the most common seal species in most refuse faunas from coastal hunter-gatherer sites dating from the late Atlantic to the early Subboreal period (ca. 4000-2000 cal B. C.) in the Baltic Sea. Our main objective was to examine the migration contra breeding population hypotheses regarding the Baltic harp seals. Analyses of epiphyseal fusion data and osteometry of archeological harp seal remains from 25 dwelling-sites suggest that a local breeding population established itself in the early Subboreal period. In the Middle Neolithic the rookery possibly was situated in the Baltic proper, south of Aland and west of Gotland. The mean adult size of the Baltic harp seals decreased, suggesting minimal genetic exchange with the north Atlantic Ocean population. Genetic drift, interspecific competition, and over-hunting by humans are all factors likely to have contributed to the eventual extinction of harp seals in the Baltic Sea.