In this study, I examined the biogeographical distribution of chloroplast and nuclear genetic diversity of Northern red oak (Quercus rubra L.) at 26 sites in the northwestern part of the species range. Chloroplast diversity is low and declines to only two lineages in the north. Loss of chloroplast diversity could be the result of repeated founder effects as glaciers advanced and retreated across North America during the last 800,000 years. In contrast, the metapopulation appears to be nearly panmictic, based on fixation indices for nuclear microsatellite polymorphisms. Private alleles were few, but most occurred in the north, suggesting that the northern and southern populations may have somewhat different disturbance histories. I detected fine-scale substructure at the northern edge of the range and found that an island population had higher allelic richness than three shoreline populations and had three private alleles not found in any of the other 25 sites suggesting that the island population has retained diversity lost elsewhere.