Northern flying squirrels (Glaucomys sabrinus) are found in boreal forests of northern and northwestern North America, but a small population is isolated to the Black Hills of South Dakota and Wyoming. Few micro satellite primers have been developed for this species, though they are needed to examine the genetic structure of these populations. Thus, we isolated and characterized 5 micro satellite loci in northern flying squirrels through a series of steps involving microbiology, molecular biology, and genetic techniques. Data analyses with these primers indicated that the northern flying squirrel population found in the Black Hills may have low heterozygosity and significant departure from Hardy-Weinberg equilibrium. The development of these primers not only provides additional data for analyzing a small, disjunct population but also serves as a mechanism for understanding population dynamics and assisting with overall management and conservation of unique populations.