Fish health and the aquatic ecosystem are strongly interwoven and interrelated. The aquatic ecosystem receives a range of anthropogenic chemicals which have toxicological or lethal health effects on the aquatic animals. The aim of this study was to determine the level of induced mutation and genomic stability of different sub-lethal doses (25%, 50% and 75% LC50) of heavy metal [Nickel (Ni), Mercury (Hg), Lead (Pb)and Zinc (Zn)] in Clarias gariepinus (Burchell, 1822) andOreochromis niloticus (Linnaeus, 1758) using RAPD-PCR technology over a period of 21 days. Four highly polymorphic RAPD markers were evaluated on isolated DNA from both heavy metal exposed fishes and control fishes after exposure. Observation of RAPD profiles in C. gariepinus revealed more damaging effect as sub lethal doses increased with zinc (a + b = 44 bands) mercury (a + b = 41 bands) nickel (a + b = 37 bands) lead (a + b = 35 bands) than with nickel (a + b = 37 bands) zinc (a + b = 34 bands) lead (a + b = 32 bands) mercury (a + b = 31 bands) for O. niloticus when compare to the control groups. Although, the genomic stability template decreased sub lethal heavy metal doses, higher stability was observed in O. niloticus (GTSPb = 26.32% GTSHg = 18.42% GTSZn = 10.53% GTSNi = 2.63%) than in C. gariepinus (GTSPb = 5.41% GTSNi = 0.0% GTSHg = -10.81% GTSZn = -18.92%). The results obtained showed differential variation in heavy metal induced   genetic mutation and genomic stabilty in C. gariepinus and O. niloticus. These observable differences might be due to the physiological structure of the fish species evaluated. This study also confirms that RAPD–PCR technology is a useful tools in detecting the genotoxic effect of heavy metals in aquatic organisms but due to low reproducibility of RAPD results, it is recommended that this technology should be used along with other molecular techniques in fish genotoxicity studies.Keywords: Heavy metals, Induced, Genotoxicity, Fish, RAPD-PCR Technique