Cytogenetic analyses of Bryconamericus aff. iheringii specimens from the upper Paraná River basin (State of Paraná, Brazil) are provided. They had 2n = 52 chromosomes and two cytotypes with variations in their karyotypic formulae: cytotype I with 12 metacentric, 18 submetacentric, 8 subtelocentric and 14 acrocentric chromosomes with a fundamental number (FN) of 90; cytotype II with 8 metacentric, 28 submetacentric, 6 subtelocentric and 10 acrocentric chromosomes with a fundamental number (FN) of 94. Differences in C- and G-band patterns between the cytotypes, distinguishing marker chromosomes for each karyotype, were reported. The R-band pattern by 5-bromodeoxyuridine incorporation was obtained in chromosomes of the cytotype II sample. In some metaphases, the second pair of submetacentric chromosomes is distinctive: its short arm is heterochromatic (positive C-band), corresponding to a late replication region. In the same cytotype, a G- and R-band size heteromorphism w as recorded in the long arm of pair 9 (submetacentric). These methodologies revealed an actual karyotypic differentiation in the B. aff. iheringii population analyzed. Morphometrical comparative analyses and a discussion of evolutionary aspects of chromosome diversification in species of this genus are provided as well.