Using microscopy and/or immunodiagnosis, the authors analyzed 284 fecal samples from the Brazilian rock cavy, Kerodon rupestris, that were collected between 1984 and 2015 in Serra da Capivara National Park for the presence of helminths and protozoa. Fourteen morphospecies of helminth eggs of the following taxa were found: Trematoda, Nematoda, Strongylidae, Lagochilascaris sp., Strongylida, Trichuris (2 species), Oxyuridae (3 species), Ancylostomatidae (2 species), and Ascarididae (2 species), along with 3 protozoan taxa: Coccidia, Cryptosporidium sp., and Balantidium sp. During the last 30 yr, the population of K. rupestris has increased in the region as a consequence of the creation and management of the National Park, and data from this study show a concurrent increase in the diversity of intestinal parasites in this host, including new reports. Some of these species have zoonotic potential, which suggests that K. rupestris may be in contact with domestic farm animals and/or human feces. These results show the importance of integrating different diagnostic approaches for the identification of protozoa in the region and indicate that further methods need to be employed to increase recovery. This work highlights the usefulness of parasite studies in assessing the health of ecosystems, especially in protected areas, which should be considered by park managers and health agencies.