Canavalia is a pantropical legume genus of lianas comprising approximately 60 species distributed in a wide range of habitats. In the last taxonomic revision the genus was divided into four subgenera: Canavalia (Pantropical) Catodonia (Neotropical excepting one species also found in the Old World) Maunaloa (Hawaiian) and Wenderothia (Neotropical). In this study we reconstructed the phylogeny of Canavalia using a broad taxon sampling and analyses of nuclear (ETS and ITS) and plastid markers (trnK/matK). We evaluated the infrageneric classification of the genus and investigated its biogeographical history using molecular dating analyses and ancestral area reconstructions. The phylogenetic analyses resolved subgenus Wenderothia as monophyletic. Subgenus Catodonia needs to be recircumscribed and the relationships between subgenera Canavalia and Maunaloa remain unclear. Canavalia arose during the Miocene with a mean stem age estimate of 13.8 Ma and mean crown age estimate of 8.7 Ma and most extant species evolved during the Pleistocene. Several climatic and geological events are chronologically coincident with the divergence of the major clades of Canavalia (glacial/interglacial periods Andes uplift and the formation of Pebas and post-Pebas systems closure of the Isthmus of Panama and change in the direction of ocean currents). Ancestral area reconstructions for the early divergence of the genus are equivocal although some evidence suggests Canavalia originated in the wet forests of South America and achieved its current pantropical distribution through recent transoceanic dispersal. The evolution of Canavalia is better explained by a series of several processes than by discrete historical events.