The floristic treatment of Engler and Diels, published in 1901, provides the only infrageneric classification of the pantropical genus Xylopia (Annonaceae). Here we test and extend that classification using molecular and seed morphology characters. Phylogenetic relationships were reconstructed using data from four plastid regions obtained from 44 of the approximately 165 species in the genus, recovering four well-supported major clades. Seed characters were examined for these taxa, and six aril morphologies, three previously undocumented, were distinguished; we also document the presence of a sarcotesta on the seeds of many species. Molecular and seed data support recognition of five sections within the genus; one, Xylopia sect. Rugosperma, is proposed here as new. Our phylogenetic results suggest an African origin for the genus and reveal complex biogeographic patterns, likely facilitated by long-distance dispersal.