There is growing evidence that populations of the northern flying squirrel (Glaucomys sabrinus) are declining in the eastern United States, perhaps due to competition with the southern flying squirrel (Glaucomys volans). Potential causes include parasite-mediated or apparent competition from the shared intestinal nematode, Strongyloides robustus, which has been shown to detrimentally affect the northern flying squirrel but not the southern flying squirrel. To investigate this hypothesis, we conducted a preliminary study on the parasite community of both flying squirrel species from sites in Pennsylvania where the two species occur sympatrically and where G. sabrinus is now considered endangered at the state level. We compared these parasite communities with those from northern flying squirrels from northern New York where the southern flying squirrel is absent. We found eight species of gastrointestinal parasites (Pterygodermatites peromysci, Lemuricola sciuri, Syphacia thompsoni, Syphacia spp., Capillaria spp., Citellinema bifurcatum, Strogyloides robustus, and an unidentifiable cestode species) in both species of flying squirrels examined for our study. The parasite-mediated competition hypothesis was partially supported. For example, in Pennsylvania, S. robustus was overdispersed in southern flying squirrels, such that a small proportion of the hosts carried a large proportion of the worm population. In addition, we found S. robustus to be present in northern flying squirrels when the species were sympatric, but not where southern flying squirrels were absent in New York. However, there was no association between S. robustus and the body condition of flying squirrels. We detected a potential parasite community interaction, as S. robustus abundance was positively associated with P. peromysci.