The climatic and environmental changes associated with the last glaciation (90,000 to 10,000 years before the present; 90 to 10 ka B.P.) are an important example of the effects of global climate change on biological diversity. These effects were particularly marked in Beringia (northeastern Siberia, northwestern North America, and the exposed Bering Strait) during the late Pleistocene. To investigate the evolutionary impact of these events, we studied genetic change in the brown bear, Ursus arctos, in eastern Beringia over the past 60,000 years using DNA preserved in permafrost remains. A marked degree of genetic structure is observed in populations throughout this period despite local extinctions, reinvasions, and potential interspecies competition with the short-faced bear, Arctodus simus. The major phylogeographic changes occurred 35 to 21 ka B.P., before the glacial maximum, and little change is observed after this time. Late Pleistocene histories of mammalian taxa may be more complex than those that might be inferred from the fossil record or contemporary DNA sequences alone.