The Sélingué hydroelectric dam is built on the Sankarani River in Mali. It is a fishing production area teeming with many fish species including Coptodon zillii. The species was selected for the study of genetic diversity. The study involved 120 specimens from two landing stages, Carrière in the lake area and Faraba near the Sankarani River. Each sample was subjected to DNA extraction from a caudal fin portion. Ten microsatellite markers were used and the genetic diversity of each locus analyzed. The results showed a number of alleles varying from 2 to 5 per marker with an average of 2.9. The loci were 70% polymorphic at the 95% cutoff. In total, 29 alleles were observed for all the samples with 2 groups on the dendrogram. Group I consists of 5% of the Faraba samples and Group II of the Carrière and 95% Faraba samples. In group II, there is a separation according to landing stages with little differentiation between the samples from the two sites. The expected heterozygosity (He=0.35) is lower than that observed (Ho=0.69), reflecting an excess of heterozygosity, with an absence of consanguinity and less significant gene exchange between the specimens of the two zones. These results show high polymorphism and genetic diversity in the samples studied. They offer basic elements on the knowledge of the genetic diversity of the species. However, the study could be extended to C. zillii populations throughout the lake and rivers.