A collection of fish bones was recovered from upper Pleistocene (Gamblian) deposits near the confluence of the Kagera and Rurubu rivers in Tanzania, west of Lake Victoria. The Rurubu/Kagera bones include two families: the Clariidae (Clarias gariepinus, Clarias sp.) and Cichlidae (tribes Oreochromini, Haplochromini; Oreochromis sp.). Geological, paleontological, and molecular data presented here provide new insights into Pleistocene eastern African biogeography and into the evolution and past affiliations of the Rurubu/Kagera and Lake Victoria fish taxa. The data indicate that the Rurubu/Kagera taxa were descended from Miocene-aged populations in the Congo and/or Nile rivers. Data also suggest that the Rurubu/Kagera haplochromines may have been part of a shared Kagera River/Lake Victoria basin haplochromine clade, whose later members radiated into hundreds of species in Lake Victoria over the past approximately 15,000 years.