In the freshwater ecosystems of Brazil can be found high biodiversity of fish, about 5160 species. However, the Jacaré-Pepira River, located in the state of São Paulo, Brazil, presents a diversity of fish still to be explored in ichthyological studies. Metazoan parasites of Pimelodus maculatus and Rhamdia quelen were qualitatively and quantitatively diagnosed. Ten species of parasites (Demidospermus sp., D. majusculus, D. bidiverticulatum, D. paravalenciennesi, Ameloblastella paranaensis, Scleroductus sp., Riggia sp., Austrodiplostomum compactum, Helobdella sp. and Neochinorhynchus pimelodi) were collected in P. maculatus and eight species of parasites (Aphanoblastella robustus, A. mastigatus, Phyllodistomum rhamdiae, Crocodilicola pseudostoma, Henneguya jundiai, Contracaecum sp., Rhabdochona sp. and Capillariidae gen. sp.) were collected in R. quelen. All parasites presented aggregate distribution. A significant correlation was observed in P. maculatus concerning the weight with the prevalence of ectoparasite D. majusculus; however, R. quelen showed a relation to the length and weight with the abundance of ectoparasite A. mastigatus and endoparasites. The parasitic community of P. maculatus and R. quelen was characterized by high diversity, high richness, and low uniformity.