Two Clariid species, Clarias gariepinus and Heterobranchus bidorsalis were compared at four loci using C. gariepinus microsatellite markers (Cga01, Cga02, Cga03, and Cga05). The heterozygosities observed were found to be 0.450 ± 0.050 and 0.442 ± 0.127, while 100% polymorphism was observed in both species. Overall, 95% of the samples amplified upon polymerase chain reaction (PCR) amplification and 44.3% of the total alleles observed for all the loci were heterozygote. Conformity to Hardy-Weinberg equilibrium using the Chi-Square test showed that 81.25% of locus-population relationship conformed to Hardy-Weinberg equilibrium. The neighbor-joining phylogenetic dendrogram obtained gave a bootstrap value of 72, indicating that the genetic distance between the two species is distinct.