Fossil elements belonging to fishes were recovered from the Pliocene Chiwondo Beds in the Malawi Rift. This is our first knowledge of fishes from Lake Malawi. The Chiwondo Bed fishes can be assigned to living taxa including lungfish (Protopterus), catfishes (Bagridae, Claroteidae and Clariidae), cichlids, and a single tooth referred to tigerfish (Hydrocynus). Although small and taphonomically biased, the assemblage shows several taxonomic differences compared with the modern Lake Malawi fauna. Most of the geographic and taxonomic affinities of the assemblage are with fishes from the African East Coast Province rivers, whereas the modern lake fauna primarily has affinities to the Zambezi River system. The Chiwondo fish assemblage contributes new information on Plio-Pleistocene eastern/southern African biogeography and waterways, and how these may have influenced faunal movements between eastern and southern Africa.