The first extensive cpDNA phylogeny of African Begonia was estimated with chloroplast trnL intron DNA sequences. A total of 81 Begonia species was sampled and analyzed using parsimony and maximum likelihood methods. Analyses showed well-resolved sectional relationships, but little resolution at the base of the phylogeny. Malagasy species of Begonia formed a monophyletic group, as were the mainland African wingless fleshy-fruited species with the exception of section Mezierea. Species in section Mezierea are not as closely related to other wingless fleshy-fruited species as once thought. The section is polyphyletic, with the Malagasy members of the section nested within the Malagasy clade. The phylogenetic position of species in section Mezierea demonstrates that fleshy fruits have evolved at least twice in African Begonia. The terrestrial, 2-tepaled, West and Central African yellow-flowered begonias and their related species are also monophyletic, with the monotypic section Cristasemen and B. iucunda holding a solitary, basal position. The predominantly East and South African species in sections Rostrobegonia, Augustia, Sexalaria, and Peltaugustia show greater affinity with Asian and American, rather than other African begonias, and are interdigitated among them; therefore African Begonia are not monophyletic. The trnL intron is a useful region for identifying monophyletic groups across the whole genus and breaking up the genus into workable units. This demonstrates the value of reconstructing phylogenies of large genera in order to achieve more stable classifications.