The phylogenetic relationships of African Begonia, in particular those of the fleshy-fruited species, were assessed by cladistic analysis of DNA sequences from the non-coding chloroplast region trnL. In addition, a morphological cladistic analysis of the fleshy-fruited species in sections Baccabegonia, Squamibegonia, Tetraphila and Mezierea was carried out to investigate relationships and character evolution. The trnL phylogeny is generally congruent with that produced from cladistic analyses of the internal transcribed spacer sequence data in a previous study, although significant incongruences between both topologies occur in the basal nodes. trnL and ITS data largely agree with existing sectional concepts based on morphology and there is overwhelming evidence from both data sets that the diversity of Begonia is geographically structured. However, sequence data has given strong evidence for some previously unsuspected relationships. Fleshy-fruits arose at least twice in Africa, refuting previous hypotheses which have suggested that fleshy-fruits represent a single evolutionary event. The position of the endemic terrestrial section from São Tomé, Baccabegonia, nested within an almost exclusively epiphytic clade suggests its derivation from an epiphytic ancestor. A new section to include B. iucunda is recommended, in light of its isolated position in the both the trnL and ITS phylogenies. This is supported by evidence from previous morphological studies. Similarly B. loranthoides, currently included in section Tetraphila, but distinct from other species in the section, particularly in fruit morphology, could possibly merit a section of its own. Morphology alone in Begonia is considered unreliable for phylogenetic reconstruction, with most characters showing high levels of homoplasy. Although most clades in the molecular trees are supported by one or more morphological characters, a small number of cryptic clades remain for which no obvious morphological characters provide synapomorphies.

Key words: Africa, Begonia, phylogeny, trnL