Information on genetic diversity is essential in fish conservation programs, the constitution of gene banks and the selection of the most efficient strains. The objective of this contribution is to identify the genetic diversity of wild populations of Clarias anguillaris from river basins in Mali. Eight microsatellite markers (Cba11, Cba19, Cba20, Cga02, Cga06, Cga10, Cm12, Cma17) were used on fins taken from 131 fish. After DNA extraction and PCR amplification, the alleles obtained are separated on a 3% metaphor gel, visualized using the E-Box device. The data was analyzed using Power Marker V3.25 software. The results identified 54 alleles with an average polymorphism information content (PIC) of 0.60. The number of alleles per locus varied between 2 (Cba11) and 10 (Cba19). The rate of heterozygosity was between 0.16±0.07 and 0.14±0.05. The average heterozygosity observed was lower than that of the expected heterozygosity, i.e. 0.16±0.037 versus 0.34±0.04. Three genotypes have been recorded. Group 1 consists of samples from Mopti (Niger Basin) and Lake Magui (Senegal Basin), group 2 those from Sankarani (Niger Basin), Lake Magui and the Bafing and Bakoye rivers (Senegal Basin) and group 3 by those of the Bafing, Bakoye and Sankarani rivers. These results indicate a genetic diversity of the species in the river basins of Mali. The information will serve as guidance in conservation programs for Clarias anguillaris in Mali.