Around 2000 fish species of the family Cichlidae (Perciformes, Teleostei) can be found in and around the three East African Great Lakes, the centers of cichlid biodiversity. Several adaptive radiations produced an abundance of species differing dramatically in their morphology, behavior and general ecology. Although Lake Tanganyika contains fewer species than Lakes Malawi and Victoria, it houses what is perhaps the most diverse assembly of cichlids. The lake?s shore habitats consist of alternating patches of rocky and sandy substrates which serve as geographic barriers and promote allopatric speciation. Due to the relative ease by which gene flow can be curbed along the structured shoreline, speciation often does not include the evolution of reproductive barriers. As a consequence, hybridization in secondary contact occurs in cichlids that inhabit the shallow waters of the lake. As opposed to the littoral habitat, the lake?s deepwater habitats are characterized by lower species diversity and fewer available niches. A lack of pronounced geographic barriers should have necessitated the early evolution of reproductive barriers between incipient species. As a consequence, we hypothesize that deepwater species should display no signs of hybridization. To test this, I constructed nuclear multi-locus AFLP phylogenies of two endemic deepwater tribes, the Bathybatini and Limnochromini, and compared them with mitochondrial phylogenies of earlier studies. Using a tree-based homoplasy excess test, I could not find any signs of hybridization in the history of these tribes, which confirmed our hypothesis. Furthermore, the nuclear phylogenies provided well supported reconstructions of the speciation patterns of the Bathybatini and Limnochromini. Both tribes underwent adaptive radiations and ecological segregation during speciation could be inferred. In both tribes, taxonomic uncertainties due to conflicting results of earlier studies could be resolved.