Parasite infection is one of the most important factors in wildlife conservation. However, fecal parasite profiles of threatened Asiatic black bears (Ursus thibetanus) are only sporadically reported, and the effect of parasitic diseases on the survival of the locally endangered Formosan black bear (Ursus thibetanus formosanus) in Taiwan remains undetermined. The study objective was to investigate the gastrointestinal parasite profiles of Formosan black bears in Yushan National Park, the only known high-density habitat for the species in Taiwan. Bear fecal samples were collected in the acorn season (from October to February) from January 2008 to October 2012. To avoid bias created by repeat sampling, the parasite profiles of fecal samples collected in 2010 from 46 individually identified bears (which were identified by genetic analysis) were also examined. Parasites were isolated by various methods and identified by morphologic characteristics. A total of 220 samples were analyzed and the results were compared between seasons, sexes, and individuals. The overall frequency of parasite infection was 77.3%, and it varied by species, with Baylisascaris transfuga infection being the most frequent. We suggest that one factor underlying the high frequency and high intensity of infection that we observed is the fact that the bears seasonally congregated at high density in a small area. To our knowledge, this is the first thorough study of gastrointestinal parasites in Asiatic black bears. The long-term nature of the investigation and the relatively stable frequency and intensity of infection suggest that parasitic diseases could serve as bioindicators of ecosystem health.