The pulmonate snails of the genus Biomphalaria are widely distributed in the tropics, and they are intermediate hosts of the digenean trematode Schistosoma mansoni that causes intestinal schistosomiasis in humans. Recent molecular evidence suggests that Biomphalaria originated in South America, and following a recent transatlantic migration colonized Africa, where it radiated into the currently recognized 12 species. In the present study we further investigate the internal phylogenetic relationships of African Biomphalaria with emphasis on the dispersal and speciation on the continent, especially in the Great Lakes in East Africa. Our results, based on 16S ribosomal DNA, cytochrome oxidase subunit I (COI), and ribosomal internal transcribed spacer I (ITS1), support the monophyly of an African clade with two separate lineages (Biomphalaria pfeifferi/Biomphalaria camerunensis and the Nilotic species complex/Biomphalaria angulosa). Following the initial colonization of Africa, Biomphalaria spread towards the east where a later radiation occurred in the Lake Victoria basin and the Albertine Rift Valley Lakes. With further dispersal along the River Nile, additional speciation took place giving origin to the North-east African species Biomphalaria alexandrina. Our results present almost no support of the species groups of Mandahl-Barth (except for the pfeifferi group), which is in accordance with other molecular appraisals. Our results suggest that Biomphalaria stanleyi, which is endemic to Lake Albert, is not an ecophenotype of the continental B. pfeifferi as previously suggested by other molecular studies. B. angulosa is sequenced for the first time and it is inferred to have an important phylogenetic position as sister group to the Albertine Rift/Lake Victoria basin radiation. © 2007 The Linnean Society of London, Zoological Journal of the Linnean Society, 2007, 151, 337–349.