Comparative cytogenetic studies were carried out on Apareiodon affinis from an important hydrographic system at South America, the Paraná river basin. Two distant regions were chosen, which were separated by Guaíra Falls (formerly Sete Quedas); the region in the upper part of the hydrographic basin is called Upper Paraná (Brazil), whereas and the other in the lower part is called Lower Paraná (Argentina). Individuals from Upper Paraná have diploid numbers of 2n = 54 (NF = 108) for males and 2n = 55 (NF = 110) for females, showing female heterogamety with a ZZ/ZW₁W₂ multiple sex chromosomes system that is endemic for the region. In different localities at Lower Paraná, the specimens presented diploid number of 2n = 54 for both sexes, without any sex chromosomes heteromorphism. However, they have an accentuated polymorphism characterized by variation in number of acrocentric chromosomes, constituting something new for family Parodontidae. The most likely hypothesis to explain the origin of such polymorphism is based on successive pericentric inversions giving rise to acrocentric chromosomes. Thus, it was possible to detect 10 cytotypes along the Lower Paraná basin. Such chromosomal variations possibly are the consequence of an adaptative process. Our data probably indicate the occurrence of distinct species in each region that share the same denomination.