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The present study was carried out to investigate the genetic differences in the Protein banding pattern of Tilapia guineensis and Sarotherodon melanotheron populations in Southwest Nigeria using Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis (SDS-PAGE). Four populations of Tilapia guineensis and three populations of Sarotherodon melanotheron from Ondo and Lagos states were considered for the study. The sarcoplasmic protein of the studied Cichlid species resolved on 12% SDS-PAGE revealed variations in their genetic diversity indices (number of alleles, shanon information index, heterozygosity and percentage polymorphism). T. guineensis had more proteins and higher genetic diversity as was revealed by the genetic diversity parameters and was found to be more polymorphic with a percentage polymorphism of 78.57% than S. melanotheron (57.14%). The two species had similarity coefficient of 0.82 indicating high genetic similarity between them. UPGMA (Unweighted Pair Group Method with Arithmetic Mean) dendrogram also revealed some level of genetic similarity between the studied populations and among the two species. Analysis of molecular variance (AMOVA) confirmed the low genetic variation among the populations of the cichlid species and demonstrated that genetic variation was mostly within populations in both species. It is established from the study that Tilapia guineensis had higher genetic diversity than Sarotherodon melanotheron and the two species are closely related. Further study involving molecular markers is encouraged to complement this finding.