Abstract: The utilization of molecular markers-assisted genetic diversity study is critical and imperative for a more robust selection and breeding programmes in aquaculture. Twenty C. gariepinus species were randomly selected, 5 each from four Rivers/locations-Okurikan (OKU), Lemna (LMN), UNICAL Fish Farm (UFF) and MCC cultured fish site, in Cross River State, Nigeria for genetic diversity study using RAPD technique. Genomic DNA extraction and purification from caudal fin tissue sample was performed using ZR Genomic DNA tissue extraction Kit, primed using OPA09, OPA11 and OPA13 RAPD primers and amplified using PCR. The amplified fragments were ran on gel electrophoresis and visualized under ethidium bromide dye. Thirty four bands were generated by the three RAPD primers from the four C. gariepinus populations of which 28 were polymorphic, accounting for 82.35%. Polymorphism revealed by each fish population ranged from 92.86-100% while, gene diversity estimates ranged from 0.246±0.16-0.385±0.09. Intra-population similarity index ranged from 42.49-78.4% while, the inter-population similarity index across all population combinations ranged from 52.32-71.69%. These result also revealed that as genetic distances increases, genetic identities narrows between the wild and the cultured species. UPGMA dendrogram generated two major clusters with C. gariepinus species from OKU, UFF and MCC in cluster-1 and C. gariepinus species from LMN in cluster-2. Implicitly though, our results suggest that there were several genetic diversity in the populations studied, especially between the cultured and the wild, which could encourage selection of C. gariepinus from OKU and LMN populations for the purpose of breeding and improvement.