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[Display omitted] • Multilocus phylogeny of Lates contradicts morphology-based phylogenetic hypotheses. • Extant African lates perches are a monophylum that started to diversify ~2–4.5 MYA. • The nile perch comprises three divergent, geographically restricted lineages. • The nile perch is paraphyletic with respect to the four Lake Tanganyika Lates species. • Lates colonized and radiated in Lake Tanganyika more recently than other fishes. Lates perches of the genus Lates (Latidae) are large piscivorous fishes, with a strikingly disjunct distribution range in coastal areas and estuaries of the Indo-Pacific region and in some large African freshwater systems. Previous phylogenetic hypotheses based on osteological and ontogenetic data suggested paraphyly of the African representatives, or even the small Lake Tanganyika species assemblage, with respect to the remaining Lates species. Based on a multilocus phylogeny, however, we show that extant African lates perches are monophyletic. The Nile perch, L. niloticus , which is widely distributed in the Nilo-Sudan region and Central Africa, comprises three distinct lineages and is paraphyletic with respect to the four endemic Lake Tanganyika species. We find that diversification of extant African Lates happened only as recently as the Pliocene. With the extensive, in part much older fossil record, this suggests repeated extinction and (re-)colonization of hydrological systems. We further find that Lates started to diversify in Lake Tanganyika only in the Pleistocene, which is much more recent than other fish radiations endemic to Lake Tanganyika, implying that they radiated in the presence of other top predators already in this ecosystem. [ABSTRACT FROM AUTHOR]