Biodiversity across a landscape is a product of both historical events and ongoing contemporary forces. The past and present factors that influence black bear Ursus americanus diversity on the Alexander Archipelago and mainland of Southeast Alaska were investigated by assessing nuclear genetic variation. The natural fragmentation of the region, the high vagility of black bears and their possible recent post-Pleistocene colonization to Southeast Alaska allowed us to discern between past and present forces characterizing diversity. Two known black bear lineages, estimated previously with mitochondrial DNA to have diverged 1.8 million years ago, remained evident in data from more rapidly evolving nuclear genetic markers. Two nuclear genetic clusters geographically correspond to the lineages, suggesting that contemporary movement since colonization (likely beginning 18 000 cybp) has not been sufficient to eliminate genetic differences between the highly divergent lineages. Concomitantly, the clearest pattern of genetic diversity is related to contemporary geographic patterns; contemporary geography differs from geography immediately after deglaciation due to sea-level change. Narrow saltwater straits, expansive ice fields, narrow beach fringes and saltwater inland bays separate genetically distinct groupings of black bears.