The present paper represents the first study on the endoparasitic fauna of Potamotrygon falkneri and P. motoro in the upper Paraná River floodplain. Fishes were collected by fishing rod and gillnetting in different stations of the floodplain, from March, 2005 to September, 2006. Parasites were sampled, fixed and preserved according to specialized literature. About half of the analyzed fish were parasitized by at least one of the following species of endoparasites: Clinostomum complanatum, Genarchella sp. and Tylodelphys sp. (metacercaria) (Digenea); Acanthobothrium regoi, Rhinebothrium paratrygoni, Paroncomegas araya and Potamotrygonocestus travassosi (Cestoidea); Brevimulticaecum sp. (larva), Cucullanus sp., Echinocephalus sp. and Spinitectus sp. (Nematoda); and Quadrigyrus machadoi (Acanthocephala). Some species were already registered in Chondrichthyes and others were previously recorded in Osteichthyes from the study area. The study listed ten new records of parasites in the host P. falkneri, one new record in the host P. motoro and five new records in the locality upper Paraná River.