Abstract: Background and Objective: Overexploitation and overfishing is one of the major factors causing depletion or extinction of commercially important fish species. In order to curb this effect, restocking and stock enhancement have been utilized to revive population of numerous species that have gone extinct or threatened in the wild. The reduction in genetic variation within the culture populations has raised worries in the use of culture population for restocking and stocking enhancement. The objective of this study was to reveal the genetic variation between cultured and wild Oreochromis niloticus and ascertained whether the cultured species can be used for restocking and stocking enhancement programme. Materials and Methods: In this study, Randomly Amplified Polymorphic DNA (RAPD) markers were used to analysis the genetic variation between 20 samples of cultured and wild Oreochromis niloticus (O. niloticus) species collected from New Bussa, Niger State. Four RAPD primers were used for the DNA amplification which generated a total of 69 band loci ranging from 750-7126 bp for cultured and wild Oreochromis niloticus. Non-parametric analysis of molecular variance (AMOVA) was used to estimate the genetic variation of cultured and wild Oreochromis niloticus within populations and among populations, using software GENALEX 6.501 and the diversity and genetic distance was determined using the same software. Results: The average percentage of polymorphic loci for cultured and wild Oreochromis niloticus was 48.87 and 49.34%, respectively. The percentage of molecular variance within and among species for cultured and wild Oreochromis niloticus was 99 and 1%, respectively, indicating the high genetic variation within species and very low genetic variation among species. The total proportion of genetic variation (PhiTP value) was 0.013 and data value was 0.281, PhiPT (0.013)<data (0.281), no significant difference. The result from PhiTP value further shows low genetic variation among cultured and wild Oreochromis niloticus. Conclusion: The high genetic variation within species is very important for species long term survival and low genetic variation among cultured and wild Oreochromis niloticus and give the possibility of using cultured species for restocking and stocking enhancement.