Samples from 861 colonies of 12 Partamona species from 125 Brazilian localities were analysed for a SCAR marker specific to the B chromosomes of P. helleri. We identified the SCAR marker in 6 of the 12 species analysed, including 2 (P. gregaria and P. chapadicola) from the pearsoni clade. This is the first report on the presence of this marker in Partamona species that are not included in the cupira clade, which indicates that the B chromosomes probably are more widespread in this genus than previously thought. The analysis revealed a high frequency of the SCAR marker in the samples of P. helleri (0.47), P. cupira (0.46), and P. rustica (0.29), and a low frequency in P. aff. helleri (0.06). The frequency of the marker in P. helleri was correlated with the latitude of the sampling locality, decreasing from north to south. Sequence data on the SCAR marker from 50 individuals of the 6 species in which the presence of this marker was shown revealed a new scenario for the origin of the B chromosomes in Partamona.