Mountain bongo (Tragelaphus eurycerus isaaci) are critically endangered antelopes found only in Kenya’s montane forests. The need to re-establish a viable, healthy and self-sustaining population is urgent. With less than 100 individuals left in the wild and rapidly declining, the impact of endoparasites remains largely unstudied. We opportunistically collected and analyzed the fecal samples from a reintroduced- population over a two-year period using random focal sampling method. Coccidia and Strongylids as the predominant gastrointestinal parasites. Infestation levels of coccidia varied significantly by season (χ2 = 1.50.707, p < 0.01) and age group (χ2 = 2, 97.471p < 0.01. Strongylids infestation exhibited significant variation only among age groups. These results expand information on endoparasite affecting the species. Researchers and health authorities are particularly concerned about endoparasites of zoonotic significance.