With c. 1400 known species, Begonia is one of the largest plant genera. In order to address the evolution of Begonia we have produced maximum parsimony and maximum likelihood cladograms for 26S and ITS sequence data. Sequences were obtained from a total of 35 species of Begonia, one species of Symbegonia and two species of Datisca. The resulting phylogenetic hypotheses suggest that the most basal members of Begonia are from Africa, with American and Asian clades nested within the paraphyletic African Begonia. Despite marked morphological heterogeneity the endemic Begonia of Madagascar and the south Indian ocean islands form a monophyletic group. As currently circumscribed, Begonia is paraphyletic with the New Guinean endemic Symbegonia nested deeply within it and most closely related to species from the Asian section Petermannia. Analysis of a smaller ITS dataset, including three accessions of Symbegonia and nine accessions of Begonia section Petermannia, further suggests that Symbegonia is nested within section Petermannia, resolving within a monophyletic clade of New Guinean species. Morphological synapomorphies of Symbegonia are reviewed and this taxon is sunk into the genus Begonia, where it is given sectional status.