Genetic diversity of the different tilapia species collected from Cairo, Giza and Fayuom in Egypt was examined by the analysis of randomly amplified polymorphic DNA (RAPD).The polymorphisms within and between three Tilapia species were assayed using 15 random primers, and 215 loci were amplified ranging from 118 to 2556bp. The results indicated that the percentage of polymorphic loci recorded 51.8%, 58.6% and 60.3% for Oreochromis niloticus, Oreochromis aureus and Tilapia zilli species, respectively. Total genetic diversity (Ht) was (0.304) and the average coefficient of genetic differentiation (Gst) was (0.583). The genetic diversity within population was the highest for T.zilli (0.249) compared to O.niloticus and O. aureus 0.219, 0.238, respectively and the gene flow between three species was 0.357. Among the three populations, Tilapia zilli appeared to be an outgroup while Oreochromis niloticus and Oreochromis aureus were genetically closer as revealed by Nei’s biased measure of genetic identity and genetic distance values. This study concluded a relatively high level of polymorphism and genetic diversity within and between the three tested Tilapia species which may be required for the adaptation of the populations to the environmental changes