Genetic and paleontological evidence are combining to provide a new and surprising picture of mammalian biogeography in southeastern Alaska. Prior to our study, the brown and black bears of the Alexander Archipelago were considered postglacial immigrants that never had overlapping ranges. Vertebrate fossils from caves on Prince of Wales Island now demonstrate that brown and black bears coexisted there (and even inhabited the same caves) both before and after the last glaciation. Differences in mtDNA sequences suggest that living brown bears of the Alexander Archipelago comprise a distinct clade and are more closely related to polar bears than to their mainland conspecifics. We conclude that brown bears, and perhaps other large mammals, have continuously inhabited the archipelago for at least 40,000 yr and that habitable refugia were therefore available throughout the last glaciation.