This study provides data on gastrointestinal parasite infections in the geographically isolated and locally fragmented Cape Peninsula baboon population and two troops from neighbouring populations in the Western Cape Province, South Africa. We obtained data on parasite diversity and prevalence from 616 faecal samples collected from over 350 individuals in eight troops between July 2006 and May 2008. We processed faecal samples using a modified formalin-ether sedimentation technique and identified nematode eggs and protozoan cysts. We recovered seven nematode genera (Trichuris sp., Oesophagostomum sp., Trichostrongylus sp., Physaloptera sp., Ascaris sp., an unidentified hookworm morphotype, and an unidentified spirurid) and eight protozoan species (Balantidium coli, Entamoeba coli, E. histolytica/dispar, E. chattoni, E. hartmanni, lodamoeba bütschlii, Endolimax nana and Chilomastix mesnili). The nematode and protozoan fauna of the Cape Peninsula baboon population was similar to both neighbouring and geographically distinct chacma baboon populations in South Africa. Parasite prevalence was variable across study sites and seasonality did not appear to have an effect on patterns of infection. The finding of the eggs of an ascarid, possibly Ascaris sp., in the Cape Peninsula baboon population represents the first report of this nematode genus in wild baboons in South Africa.