Premise of the study: The genus Medicago, with about 87 species, includes the model legume species M. truncatula, and a number of important forage species such as M. sativa (alfalfa), M. scutellata (snail medic), and M. lupulina (black medic). Relationships within the genus are not yet sufficiently resolved, contributing to difficulty in understanding the evolution of a number of distinguishing characteristics such as aneuploidy and polyploidy, life history, structure of cotyledons, and number of seeds per fruit. •

Methods: Phylogenetic relationships of 70-73 species of Medicago and its sister genus Trigonella (including Melilotus) were reconstructed from nucleotide sequences of the plastid trnK/matK region and the nuclear-encoded GA3ox1 gene (gibberellin 3-β-hydroxylase) using maximum parsimony and Bayesian inference methods. •

Key results: Our results support certain currently recognized taxonomic groups, e.g., sect. Medicago (with M. sativa) and sect. Buceras. However, other strongly supported clades-the "reduced subsection Leptospireae clade" that includes M. lupulina, the "polymorpha clade" that includes M. murex and M. polymorpha and the "subsection Pachyspireae clade" that includes M. truncatula-each of which includes species presently in different subsections of sect. Spirocarpos, contradict the current classification. •

Conclusions: These results support the hypothesis that some characters considered important in existing taxonomies, for example, single-seeded fruits that have arisen more than once in both Medicago and Trigonella, are indeed homoplastic. Others, such as the 2n = 14 chromosome number, have also arisen independently within the genus. In addition, we demonstrate support for the utility of GA3ox1 sequences for phylogenetic analysis among and within closely related genera of legumes.