The genus Glaucomys (New World flying squirrels) is currently considered to be comprised of 2 species, the northern flying squirrel (G. sabrinus) and the southern flying squirrel (G. volans). We synthesize new information from mitochondrial DNA (mtDNA) control region sequences and microsatellite data to demonstrate that the genus consists of 3, rather than 2 species, and that Glaucomys sabrinus, as currently recognized, is actually composed of 2 separate, apparently non-hybridizing species. Control region mtDNA data from 185 individuals across North America revealed 2 distinct clades embedded within G. sabrinus: a widespread “Continental” lineage and a more geographically restricted “Pacific Coastal” lineage. The geographic distributions of these 2 lineages are largely mutually exclusive, with sympatry observed at only 3 sites in the Pacific Northwest. Analysis of 8 microsatellite loci showed no evidence of hybridization between the 2 lineages of G. sabrinus in the region of sympatry. This lack of gene flow is noteworthy given that populations of the Continental lineage of G. sabrinus have been shown to hybridize with G. volans in southeastern Canada. Finally, phylogenetic analyses and estimates of divergence times show that G. volans and Continental G. sabrinus are actually sister taxa that diverged from one another more recently than either did from Pacific Coastal G. sabrinus. We propose that these observations provide strong evidence for a third, previously unrecognized species of North American flying squirrel, whose geographic range extends along the Pacific Coast from southern British Columbia to southern California. Glaucomys oregonensis (Bachman, 1839), whose type locality is in Oregon, is the senior available name for this taxon. We propose that this newly recognized species be given the common name “Humboldt's flying squirrel.”