Northern flying squirrel (Glaucomys sabrinus) and red squirrel (Tamiasciurus hudsonicus) populations are endemic to northern North America, including the Black Hills. The Black Hills populations are considered disjunct from other populations within their range. We examined insular populations to determine whether arboreal squirrels in the Black Hills each represent a unique population. We trapped and collected ear samples from northern flying and red squirrels in the Black Hills and in areas of Montana, Wyoming, Idaho, Utah, Minnesota, and Wisconsin to infer population phylogenies with special consideration of the Black Hills population. Microsatellite loci and two mtDNA sequences were used for phylogenetic data analyses, including neighbor-joining and maximum likelihood trees, percent divergence, and nucleotide diversity. For northern flying squirrels,mtDNA phylogenetic trees grouped individuals in the Black Hills population, suggesting extended isolation from other nearby mountain ranges. In both squirrels, phylogenetic trees inferred with nDNA provide similar topologies to the mtDNA of northern flying squirrels. Sequence divergence distances (range 0 to 1.0) for cytochrome-b among studied populations were relatively small (0.00 to 0.55 [northern flying squirrel] and 0.00 to 0.01 [red squirrel]), so divergence may be from an historical event. Nucleotide diversity (cytochrome-b) was higher than in some other ranges (0.07 [northern flying squirrel] and 0.08 [red squirrel]); however, heterozygosity was low in the Black Hills populations. These data suggest that northern flying squirrel and red squirrel populations in the Black Hills Mountains are not only geographically disjunct, but genetically unique from their conspecifics elsewhere
