The protozoans Toxoplasma gondii and Sarcocystis spp. (Sarcocystidae: Apicomplexa) affect a wide variety of vertebrates. Both have been reported to infect pinnipeds, with impacts on health ranging from inapparent to fulminant disease and death. However, little is known regarding their infections and associated pathology in South American pinnipeds. We used histological techniques to survey for the presence of T. gondii and Sarcocystis spp. in 51 stranded pinnipeds from Brazil. Immunohistochemical and molecular assays were employed in those cases consistent with Sarcocystidae infection. T. gondii cysts were detected in the central nervous system and heart of a South American fur seal Arctocephalus australis, associated with meningoencephalitis, myocarditis and endocarditis, and confirmed by immunohistochemistry. Additionally, this animal presented Sarcocystis sp. cysts in brain and heart tissues. Four additional specimens-2 Subantarctic fur seals A. tropicalis, an Antarctic fur seal A. gazella and another South American fur seal-presented intrasarcoplasmic cysts compatible with Sarcocystis spp. in muscle samples. There was no inflammation associated with the Sarcocystis spp. tissue cysts and all cysts were negative for S. neurona immunohistochemistry. The B1 gene of T. gondii was amplified in the 5 pinnipeds infected by Sarcocystidae protozoans. To our knowledge, this is the first report of toxoplasmosis in wild South American pinnipeds and of Sarcocystis spp. in South American fur seals. Detection of terrestrial parasites in aquatic mammals could be an indicator of their presence in the marine environment.