The data used by Lynch Alfaro et al. (2012a, Journal of Biogeography, 39, 272–288) and the biogeographical hypothesis postulated by these authors to explain the current distribution of capuchin monkeys were reanalysed including additional cytochrome b data from Sapajus xanthosternos and Sapajus flavius. Our reconstructed phylogeny placed S. xanthosternos in a monophyletic clade representing the most basal lineage of this genus. All analyses indicated polyphyletic arrangements for several capuchin species, suggesting that incomplete lineage sorting has occurred during their evolution. These results also suggest that available molecular data lack adequate variation for accurately resolving species relationships. These results suggest that the divergence of capuchin monkey genera may have occurred in the Atlantic Forest. However, a more conclusive scenario and better resolution of the species tree requires correct identification of species, data from several unlinked nuclear loci from a higher number of individuals per species, and careful analysis of ancient DNA data from museum specimens.