Cytochrome-b sequence data of mitochondrial DNA (mtDNA) were used to infer evolutionary and biogeographic histories of the New World flying squirrels, Glaucomys sabrinus and G. volans. Two distinct mtDNA lineages were recovered within G. sabrinus: a western lineage consisting of populations from western California, Oregon, and Washington, and a much larger "eastern" Lineage comprised of populations from the remainder of the species' range (North Carolina, West Virginia, Michigan, Utah, Alaska, eastern Washington, British Columbia, and Alberta). In contrast, only one major mtDNA lineage was recovered within G. volans. Little sequence variation was observed among populations of G. volans (less than or equal to 0.6%), but sequence variation within G. sabrinus was much higher (2.3% and 2.6% within the eastern and western clades, respectively, and 4.3-7.2% between the two clades). The level of sequence divergence observed between the eastern and western mtDNA clades of G. sabrinus (4.3-7.2%) was slightly greater than that observed between the two species, G. sabrinus and G. volans (4.0-6.1%), suggesting the possibility of an unrecognized species within G. sabrinus. Minimum levels of sequence divergence among the three mtDNA clades were nearly equal (ca. 4% in all pairwise comparisons), suggesting that Glaucomys underwent a relatively rapid diversification in the early-to-middle Pleistocene. The mtDNA discontinuity in the Pacific Northwest within G. sabrinus is congruent with similar disjunctions in a variety of vertebrate taxa, suggesting that an ancestral North American boreal ecosystem may have been divided into two distinct communities at this time.