Difficulties in interpreting the evolutionary significance of Lake Malawi cichlid morphologies led us to examine molecular techniques for resolving relationships among closely related species. Mitochondrial DNA (mtDNA) sequence variation in the first half of the control region (445 bp) was examined within and between two species of Melanochromis, a genus of rock-dwelling cichlids from Lake Malawi, Africa. The mean number of pairwise differences observed within Melanochromis auratus (Boulenger) and Melanochromis heterochromis Bowers and Stauffer mtDNA haplotypes was 2.0 (0.45%) and 5.0 (1.13%), respectively, and a mean of 4.9 (1.11%) pairwise differences between the two species was observed. Mean pairwise differences between Melanochromis species and Pseudotropheus zebra (Boulenger), another species of rock-dwelling cichlid and Tramitichromis cf. liturus, a sand-dwelling genus, were 11.2 (2.52%) and 21.9 (4.93%), respectively. Species divergence and radiation within the genus Melanochromis appears to have occurred rapidly and recently. Mitochondrial DNA sequence variation within this genus was sufficient for generating hypotheses concerning the evolutionary relationships within the genus and for examining generic-level relationships within and among the major cichlid lineages in Lake Malawi.