This paper characterizes the systematic positions of Medicago edgeworthii and M. archiducis-nicolai. The combined data set of chloroplast trnK/matK, nuclear GA3ox1 and ITS sequences provided a substantial amount of informative characters. The methods of Maximum parsimony, Bayesian inference, and Maximum likelihood were employed. The results showed that M. edgeworthii formed a monophyletic group with M. biflora and M. brachycarpa, both of which are members of section Lunatae; M. archiducis-nicolai is closely related to M. platycarpa and M. ruthenica. Our study supports the previous view that M. edgeworthii belongs to section Lunatae, and M. archiducis-nicolai belongs to section Platycarpae. In addition, the study suggests that M. lupulina is a member of a clade having M. tenoreana and M. minima, which indicates that M. lupulina and M. secundiflora should probably not be placed in the same section.