Thirty Lates niloticus (Linnaeus, 1758) from three Nigerian waterbodies were genotyped on six RAPD primers and fi ve microsatellites loci. RAPD revealed that eff ective number of alleles (AE) at population level per locus was within the range of 1.641 ± 0.066 to 1.645 ± 0.041 while the mean number of alleles (AN) across populations equals 2.000. Characterization on fi ve microsatellites loci revealed genetic diversity within and among studied populations. Observed heterozygousity (HO) was within the range of 0.317 ± 0.335 to 0.523 ± 0.315 while expected heterozygousity (HE) was within the range of 0.414 ± 0.306 to 0.715 ± 0.097. Proportion of diff erentiation (FST) within populations was 0.236. Overall gene fl ow (Nm) among populations equals 0.806. This study established the successful use of RAPD and microsatellite as tools for studying population structure of fi sh species, especially L. niloticus. Th us, it can be concluded that L. niloticus in the three (3) sampled Nigerian waterbodies is undergoing evolution.