The species flocks of cichlid fishes in the lakes of East Africa are the most spectacular example of adaptive radiation among living vertebrates. Similar highly derived morphologies are found among species in different lakes. These similarities have been variously interpreted either as evidence for migration of ancestral species between the lakes, or of striking convergence of morphology. To distinguish among these competing hypotheses we sequenced a portion of the mitochondrial DNA control region from six pairs of morphologically similar taxa from Lakes Malawi and Tanganyika. Our results clearly indicate a separate origin of these morphologies in the two lakes. They also suggest that the Tanganyikan radiation is relatively old, and that the species flocks in lakes Malawi and Victoria are derived from one of the ancient lineages found in Lake Tanganyika. These findings have important implications for understanding the pattern of morphological and behavioral evolution in these fish.