While the modern freshwater fish fauna of Africa has been the subject of considerable biological attention, there are few studies on the biogeography that include recent fossil reports. Since the publication of comprehensive reviews of Cenozoic freshwater fish faunas in Africa by Greenwood in the mid 1970s and updates in the late 1970s by Van Couvering, considerable collection and reporting of Cenozoic Africa fish has occurred. These specimens and reports have provided a considerable database from which to derive zoogeographical and biogeographical inferences. A pan‐African fish fauna can be documented at the generic level throughout the Miocene in northern, central and eastern Africa, including Protopterus, Polypterus, Labeo, Alestes/Brycinus, Clarias/Heterobranchus, Synodontis, and Lates. The extinct genus Semlikiichthys (formerly Lates) may also be included in this pan‐African fauna. Where the Miocene fish records were widely distributed through much of the African continent and were primarily fluvial‐derived faunas, the Early Pliocene record is strictly a central and eastern one, mainly from lacustrine deposits. These reflect the new lacustrine habitats created through severe tectonic change, in the form of rifting and volcanism. The Pliocene faunas are characterised both by extinct taxa not previously recorded, and by immigrant taxa. By the Pleistocene the Rift systems were completely formed. However, ongoing volcanism and tectonics continued to alter the hydrological systems. In the Early and Middle Pleistocene, Lakes Albert and Edward both still had the widespread modern genera Lates and Synodontis, and several taxa known from previous deposits. However, all extinct taxa had disappeared, except Sindacharax (Characidae), which was still found in Lake Edward. In the Turkana Basin, there is continuity of most taxa from the Pliocene (except for Semlikiichthys, which is absent), as well as Miocene and Pliocene Sindacharax species. In the Middle Pleistocene, Sindacharax disappears from the African fossil record. Also, in the Pleistocene, several hydrological systems lose their pan‐African faunas, including Lake Edward, Lake Victoria and the Maghreb. The modern faunas are not as diverse at the family level as previously. This history of the Neogene African fish fauna is necessarily incomplete without fossil records from many regions of Africa, particularly in the west and south.