Zambian rivers belong to two major drainages: the Luapula-Congo and the Zambezi River system. Tectonic activity repeatedly altered drainage systems in Africa, so that current fish faunas can only be understood in the context of historic drainage capture events. We use phylogenetic relationships of one widespread lineage of haplochromine cichlids, the serranochromines, to trace their biogeographic expansion and diversification in Zambia. The mitochondrial DNA phylogeny suggests five ancient clades, and their common ancestor was likely to have invaded from the Lower Congo River. The branching intervals in the linearized tree analysis suggest three major cladogenesis events and two periods of faunal exchange. The five clades originating in the Congo River drainage diversified further; one stayed in the Congo drainage, one diversified in the Zambezi system only, while the three clades of mixed distribution underwent diversification in the Zambezi system, to re-enter the Congo drainage very recently, as indicated by sometimes zero mutation differences among taxa from different drainages. Our hypothesis is consistent with the suggested radiation in the extinct Lake palaeo-Makgadikgadi, so that we propose that the Zambian serranochromine fauna in part represents survivors of the extinct lacustrine flock plus several novel species that originated in situ.