The cichlid species" flocks" which are endemic to the East African Rift Valley are characterized by frequent lineage splitting events which have led to the rapid evolution of high levels of taxonomic diversity. Changes in water level cause these habitat patches to be chronically unstable, hypothetically speeding the process of genetic differentiation through the combined effects of genetic drift and selection. Allele frequencies at four simple sequence repeat loci indicate low levels of gene flow in two rock dwelling fish species, Melanochromis auratus and Labeotropheus fuelleborni, collected from the Nankumba Peninsula in southern Lake Malawi. Small interruptions in habitat cause low, but statistically significant genetic differentiation among populations. The highest levels of interpopulation heterogeneity were observed between populations separated by deep troughs of open water. Differences in habitat usage cause the absolute magnitude of interpopulation heterogeneity to be higher among M. auratus populations than among L. fuelleborni populations. A correlation exists between allelic diversity at a locus and the relative age of a habitat, suggesting that mild bottlenecks are associated with colonization. Simulation studies indicate that the level of differentiation observed among these populations is unlikely to be merely an artifact of modest sample sizes and highly polymorphic loci.