Competition is a driving factor in shaping ecological communities and may act directly or indirectly through apparent competition. We examined a classic example of parasite-mediated competition between northern (Glaucomys sabrinus) and southern flying squirrels (G. volans) via the intestinal nematode, Strongyloides robustus, and tested whether it could act as a species barrier in a flying squirrel hybrid zone. We live-trapped flying squirrels (G. sabrinus and G. volans), grey squirrels (Sciurus carolinensis), red squirrels (Tamiasciurus hudsonicus), and chipmunks (Tamias striatus) from June–September 2019 at 30 woodlots in Ontario, Canada. Fecal samples from squirrels were collected and analyzed for the presence of endoparasite eggs. For each individual, we calculated Scaled Mass Index (SMI) as a measure of body condition to assess the effect of S. robustus on squirrels. We found eggs of S. robustus in all species except chipmunks. Infection with S. robustus did not appear to affect body condition of southern flying squirrels and grey squirrels, but we did find a weak negative effect on northern flying squirrels and red squirrels. Despite a weak asymmetric effect of S. robustus on flying squirrels, we did not find any evidence that parasite-mediated competition could lead to competitive exclusion from woodlots. Furthermore, S. robustus eggs were common in feces of the red squirrel, a species largely sympatric with northern flying squirrel.