The bearded manakins in the genus Manacus are lekking, neotropical passerines. Male plumage colour varies with geographical location and classification is based solely on these plumage patterns. It has recently been suggested that in this group of birds, plumage patterns may be a misleading taxonomic character. In this study we used microsatellite variation in a collection of museum samples to establish the amount of genetic divergence between the previously described bearded manakin species/subspecies. We found substantial genetic substructuring between species/subspecies and that plumage patterns indeed may be a misleading taxonomic character because the presence of yellow in male nuptial plumage is found in most divergent forms. We did not detect a significant isolation by distance relationship although the P-value was close to significance. Physical barriers such as rivers and mountains may affect gene flow and play a role in shaping genetic structure of the genus Manacus. Accordingly, boundaries between species/subspecies often coincide with large rivers, mountains and seas. © 2004 The Linnean Society of London, Biological Journal of the Linnean Society, 2004, 81, 439–447.