Macroptilium (Benth.) Urb. is a neotropical legume genus from the subtribe Phaseolinae. The investigated species present a stable chromosome number (2n = 22), but differ in their karyotype formulae, suggesting the presence of chromosome rearrangements. In this work, we comparatively analysed the karyotypes of six species (M. atropurpureum, M. bracteatum, M. erythroloma, M. gracile, M. lathyroides and M. martii) from the two main clades that form the genus. Heterochromatin distribution was investigated with CMA/DAPI staining and fluorescent in situ hybridization (FISH) was used to localise the 5S and 35S ribosomal DNA (rDNA) sites. Single copy BACs (Bacterial Artificial Chromosomes) previously mapped in the related genera Phaseolus L. and Vigna Savi were used to establish chromosome orthologies and to investigate possible rearrangements among species. CMA+/DAPI- bands were observed, mostly associated with rDNA sites. Additional weak, pericentromeric bands were observed on several chromosomes. Although karyotypes were similar, species could be differentiated mainly by the number and position of the 5S and 35S rDNA sites. BAC markers demonstrated conserved synteny of the main rDNA sites on orthologous chromosomes 6 and 10, as previously observed for Phaseolus and Vigna. The karyotypes of the six species could be differentiated, shedding light on its karyotype evolution.