Phylogenetic relationships among the genera Dalbergia, Machaerium, and Aeschynomene were investigated with sequences from both the chloroplast DNA trnL intron and the nuclear ribosomal DNA ITS/5.8S region. A parsimony and Bayesian analysis of individual and combined data resolved a monophyletic Dalbergia that is sister to a clade comprising Aeschynomene sect. Ochopodium and Machaerium. Aeschynomene sect. Aeschynomene is paraphyletic with respect to genera such as Bryaspsis and Soemmeringia, which collectively are sister to the Dalbergia-Machaerium-Ochopodium clade. This study identifies the disparate lineages of the genus Aeschynomene and reveals that species with basifixed stipules (i.e., sect. Ochopodium) perhaps should be ranked as a distinct genus. Species of Ochopodium have the general lomented fruit morphology in contrast to the unique indehiscent samara fruits of Machaerium. The findings of this analysis also have some bearing at the infrageneric level. Limited sampling of Dalbergia sects. Triptolemea and Ecastaphyllum resolves them as monophyletic. In contrast, the traditional infrageneric classification of Machaerium does not show much agreement with molecular groups. Additional sampling of Aeschynomene and Machaerium species, other DNA sequences, and morphological data are needed to resolve the exact relationship of sect. Ochopodium to Machaerium, as well as validate the infrageneric classification of Machaerium.