The enormous diversity of Lake Tanganyika with its cichlid and non-cichlid fish species flocks and its importance as cradle and reservoir of ancient fish lineages seeding other radiations, has resulted in a significant body of literature in the fields of biodiversity and evolution. The lake also contains several invertebrate taxa that underwent radiation in situ. Remarkably, virtually no research was carried out into the Tanganyika parasite fauna. Parasitism is the most common lifestyle on Earth in terms of species diversity, and it is established in speciation biology that parasites are prone to radiate. Hence, parasitic organisms seem a high-potential subject for speciation studies in ancient lakes. We introduce the diversity and speciation of monogenean flatworms infecting Tanganyika cichlids. Monogenea was chosen because of the species richness and host-specificity of its representatives. Their simple (one-host) life cycle ensures a tight association with the respective host species. Therefore, these parasites constitute prime markers for coevolutionary processes and host taxonomy and evolution. We set off focusing on the radiation of the endemic tropheine cichlid tribe. Combining molecular sequence data (nuclear ITS rDNA, mitochrondrial cox1) and morphological identification (using hard parts of attachment and copulatory organs), we discovered high host-specificity in monogeneans belonging to Cichlidogyrus (Ancyrocephalidae) parasitizing tropheines. Co-speciation and within-host speciation caused this genus to surpass the species richness of its host radiation. Conversely, speciation in the monogenean Gyrodactylus (Gyrodactylidae), owing to its unique life history and colonization strategy, is more influenced by host-switching. Investigating other host lineages demonstrated that monogeneans followed different speciation pathways in other cichlid tribes, e.g. lacking the host-specificity found for tropheine Cichlidogyrus parasites. We hypothesize that the relatively low mobility of rock-dwelling cichlids, and the particular host and parasite biology jointly mediate parasite biodiversity, a hitherto disregarded component of the famed species richness of the African Great Lakes. MPMV, AS, IP, MM and MG are funded by the Czech Science Foundation P505/12/G112 (ECIP), and SK and CS by the Austrian Science Fund (FWF). MPMV and MVS were PhD fellows, and TH a post-doctoral fellow, respectively, of the Research Foundation Flanders (FWO-Vlaanderen). Fieldwork was supported by FWO-Vlaanderen and the King Leopold III Fund for Nature Exploration and Conservation.