Crotalaria is a large genus of 702 species with its centre of diversity in tropical Africa and Madagascar and secondary radiations in other parts of the world. The current infrageneric classification system is based on morphological and morphomet- ric studies of the African taxa only and is here re-evaluated using a phylogenetic approach. DNA sequences derived from the nuclear ITS and the plastid matK, psbA-trnH and rbcLa markers were analyzed using parsimony and model-based (Bayesian) approaches. The resultant molecular phylogeny allowed for a new interpretation of diagnostically important morphological characters, including specialisations of the calyx, keel, standard petal and style, which are variously convergent in several unrelated infrageneric groups. Of particular interest is the congruence between the new phylogeny and the distribution of stand- ard petal callosity types. A sectional classification system for the entire genus is proposed for the first time. The new system that is formalised here comprises eleven sections: Amphitrichae, Calycinae, Crotalaria, Geniculatae, Glaucae, Grandiflorae, Hedriocarpae, Incanae, Schizostigma, Borealigeniculatae and Stipulosae. Sectional limits of the Geniculatae, Calycinae and Crotalaria are modified. The subsections Stipulosae, Glaucae and Incanae are raised to sectional level, while some groups previously recognized as subsections are abandoned due to non-monophyly (subsections Chrysocalycinae, Hedriocarpae, Macrostachyae and Tetralobocalyx). Two new sections are recognized, Amphitrichae and Borealigeniculatae.