I summarize our current understanding of the evolutionary origin and biogeographic history of the New World flying squirrels (Glaucomys). The emerging synthesis of flying squirrel systematics supports a monophyletic origin for the group in the early Miocene followed by a divergence of New World and Eurasian flying squirrels in the late Miocene. Today, the New World flying squirrels consist of 2 recognized species, G. sabrinus and G. volans. These 2 species are closely associated with the northern coniferous and deciduous hardwood forest biomes of North America, respectively, making them especially useful as biogeographic indicator species for these 2 forest types. Molecular systematic studies have revealed the presence of 2 distinct evolutionary lineages within G. sabrinus (a widespread Continental lineage and a more geographically restricted Pacific Coastal lineage). Bacular morphology and data from nuclear loci suggest recent or ongoing gene flow between these 2 lineages where they meet in the Pacific Northwest of North America. Populations of G. volans from eastern North America represent a 3rd distinct lineage within the genus. Mesoamerican flying squirrels (traditionally considered to be southern forms of G. volans) have not been examined with molecular data and may represent 1 or more additional lineages. From a biogeographic perspective, Quaternary climatic fluctuations and associated changes in the location and extent of forest habitats appear to have been important factors in promoting early evolutionary diversification within the genus; structuring of intraspecific patterns of genetic variation; and producing geographically isolated peripheral populations in high-elevation habitats at the southern extremes of each species' range, several of which are now of conservation concern. These results have broad implications for understanding the Quaternary biogeography of the coniferous and deciduous forest biomes of North America.