Cichlid fishes of the great East African lakes have been the subject of many evolutionary studies over the last decades. Over 100 haplochromine species have been described from Lake Victoria alone, many of which are endemic to that lake. Two recent studies, using enzyme electrophoresis, could not detect any genetic differentiation among the examined species. Consequently, it was concluded that the gene loci which were scored in these studies were not relevant to the genetic changes which occurred during speciation. Analyses of general protein electrophoretic patterns, however, does reveal differentiation on the supraspecific level. Three basic species groups can be discerned, each associated with ecological characteristics of these species such as diet and substratum. Implications for haplochromine evolution and taxonomy are discussed. Our data seem to support the hypothesis that trophic differentiation may have occurred within habitats, implying the possible importance of sympatric speciation in haplochromine evolution in Lake Victoria.