Siparunaceae comprise Glossocalyx with one species in West Africa and Siparuna with 65 species in the neotropics; all have unisexual flowers, and 15 species are monoecious, 50 dioecious. Parsimony and maximum likelihood analyses of combined nuclear ribosomal ITS and chloroplast trnL-trnF intergenic spacer sequences yielded almost identical topologies, which were used to trace the evolution of the two sexual systems. The African species, which is dioecious, was sister to all neotropical species, and the monoecious species formed a grade basal to a large dioecious Andean clade. Dioecy evolved a second time within the monoecious grade. Geographical mapping of 6,496 herbarium collections from all species sorted by sexual system showed that monoecy is confined to low-lying areas (altitude < 700 m) in the Amazon basin and southern Central America. The only morphological trait with a strong phylogenetic signal is leaf margin shape (entire or toothed), although this character also correlates with altitude, probably reflecting selection on leaf shapes by temperature and rainfall regimes. The data do not reject the molecular clock, and branch lengths suggest that the shift to dioecy in the lowlands occurred many million years after the shift to dioecy in the ancestor of the Andean clade.