The marine-derived stingrays of Potamotrygonidae, endemic to South American river systems, host an interesting parasite fauna equally related to marine lineages. Among those lineages, the diversity and phylogenetic relationships within Potamotrygonocotyle – a monocotylid monogenoidean specific to potamotrygonids – are poorly known, since 9 of 10 species attributed to this genus have been described in the past 3 years. Here, we readdress the diversity of Potamotrygonocotyle after examining the gills of 436 potamotrygonid individuals representing 12 described and 14 potentially undescribed species of freshwater stingrays from 19 major river systems of South America (i.e. sub-basins). We recognized 12 valid species within the parasite genus, of which four are described in this study. Our taxonomic decisions were based on the phylogenetic analysis of 14 ingroup terminal taxa and 12 morphological characters, which resulted in the following hypothesis of sister-group relationships: ((P. dromedarius, P. tatianae sp. nov.), (P. rionegrense, P. auriculocotyle sp. nov., ((P. quadracotyle, P. umbella), (P. septemcotyle sp. nov., (P. chisholmae, P. uruguayense)), (P. tsalickisi, P. eurypotamoxenus, P. rarum, (P. tocantinsense sp. nov., P. aramasae))))). According to our hypothesis, the absence of autapomorphic features for some nominal species, and the re-evaluation of morphological variation among populations, led us to consider P. eurypotamoxenus and P. uruguayense as junior synonymys of P. tsalicksi and P. chisholmae, respectively. Finally, we address the importance of biogeographic and host representation, in order to fully understand the patterns of morphological variation and host specificity within this group. We found that hypotheses of species delimitation depend greatly on efforts to sample specimens throughout its distributional range and that host specificity within this genus varies dramatically among lineages.