Captive chimpanzees living in confined environments like sanctuaries or primatology centers are frequently affected by gastrointestinal parasites. Some of these are likely to be transmitted to humans and may seriously affect public health. However little information is currently available on the gastrointestinal parasites of primates living in such environments. Here, we characterize the diversity and prevalence of gastrointestinal parasites in two populations of captive chimpanzees living in southeastern Gabon. Our study reveals that at least nine parasite species infect the chimpanzees with high prevalence, including several helminths (Ascaris spp., Enterobius spp., Strongyloides spp., Trichuris spp., Hymenolepis spp., Mammomonogamus spp), three protozoa (Balantioides spp., Entamoeba spp. and Troglodytella spp) and several unidentified parasites. All the parasite taxa we identified had previously been identified in other primates, including humans. Age, sex and site type may influence infection rates and/or parasite diversity found in a particular host.