Ovule development, megasporogenesis and megagametogenesis were studied in Macroptilium bracteatum, Phaseolus augusti, P. vulgaris var. aborigineus and Vigna adenantha to elucidate their taxonomic position. The ovule is anacampylotropous, bitegmic and crassinucellate. Megaspore tetrads are linear in M. bracteatum and T-shaped in the other three species. In all species the chalazal megaspore produces an embryo sac of Polygonum type. The results are discussed in relation to the current taxonomic classification. Our findings support the position of Macroptilium as a separate genus and the inclusion of V. adenantha in the genus Phaseolus. This is the first report of the use of embryological characters to solve intergeneric relationships of the Phaseolus-Vigna-Macroptilium neotropical complex, pointing out the method’s usefulness.