Abstract: The genomes of a natural and a cultured population of Oreochromis niloticus from each of Northern and Southern Nigeria were comparatively assessed in this study to determine the levels of genetic variation and establish their suitability as sources of broodstocks for aquaculture. DNA was obtained from clipped caudal fins and analysed in a Multigene Gradient thermocycler using 8 microsatellite markers. The amplicons generated were subjected to fluorescent genotyping and the corresponding allele scored. The data obtained was used to determine genetic parameters. While the heterozygousities of the two populations from the wild deviated from Hardy-Weinberg equilibrium (HWE), the heterozygosities of the cultured populations were within HWE. Three populations were inbred while one population was outbred. The fish obtained from these fish farms are generally not managed based on modern population genetic principles although the wild population from New Bussa is a suitable source of Nile Tilapia broodstocks for aquaculture.