Potamotrygonidae is the representative family of South American freshwater elasmobranchs. It is a monophyletic group containing 20 species grouped into three genera. Three species belonging to two genera of this family were collected from the middle Negro River, Amazonas, Brazil, and studied cytogenetically: Paratrygon aiereba, Potamotrygon motoro and Potamotrygon orbignyi. Paratrygon aiereba presented 2n = 90 chromosomes and 4M+2SM+10ST+74A. Both species of Potamotrygon presented 2n = 66 chromosomes and differed in their chromosomal formulas: P. motoro had 18M+12SM+10ST+26A and P. orbignyi had 22M+10SM+8ST+26A. No sex heteromorphism was detected. The Fundamental Number (FN) was 106 for the three species. A system of multiple NORs was found in the three species, but with interspecific differences in terms of location and position of the active Ag-NORs sites. Paratrygon aiereba presented only four sites on the short arms of two chromosomal pairs, both in terminal regions. Potamotrygon motoro presented seven sites, on the long and short arms, all in terminal regions of non-homologous chromosomes; P. orbignyi presented eight sites on the long arms, all in terminal regions, of non-homologous chromosomes. The constitutive heterochromatin was in pericentromeric regions of all chromosomes, and no significant interspecific difference was found in relation to this marker.