This study employed microsatellite DNA markers on cultured fast- and slow-growing strains of an important freshwater catfish, Clarias gariepinus from four populations in Southwestern Nigeria with a view to providing information on their genetic variability in relation to growth performance. Genomic DNA was extracted from the blood of each individual fish from the selected groups following standard procedures. The DNA sample collected was then amplified in a thermocycler using Cga01, Cga02, Cga03, Cga05, Cga06, Cga09, and Cga10 markers. The amplicons generated were subjected to genotyping and the corresponding alleles scored. The higher fixation index values identified in the slow-growing strains of adult C. gariepinus indicated the existence of a small number of heterozygote genotypes and an excess of homozygote genotypes compared to the fast-growing strains of adult C. gariepinus, suggesting that heterozygosity confers better growth performance. The C. gariepinus fast-growing strains also had higher genetic variability than the slow-growing populations. The Cga02 locus was identified as the specific locus on which significance levels were consistently expressed. Thus, it may be a potential locus for breeding studies of C. gariepinus. Analysis by Chi-square tests across all loci and populations revealed that not all the seven loci conformed to Hardy-Weinberg equilibrium in each population.