This study assessed morphological variations of Oreochromis niloticus, Sarotherodon galilaeus and Coptodon zilli collected from the Nile and its tributaries. Nineteen morphometric measurements were recorded from each specimen. Data was subjected to discriminant function (CDF) analysis, Wilks' lambda test, t-test and Leave-one-out crosses validation to determine rate of divergence among species. The t-test showed wide variability in the significance (p>0.05 to p0.01) species and site wise in morphometric trait/total length and morphometric trait/head length. The body weight/standard length ratio was consistently significant (p<0.05). Function 1 and Function 2 of CDF clearly separated between O. niloticus and S. galilaeus from Sinnar as well as in Al Sabaloga, and between O. niloticus and C. zilli from Khashm El Girba as revealed by the high significance of Wilks lambda (p<0.003, p<0.000 and p<0.000, respectively). Based on 19 morphometric traits Leave-one-out reclassified the cross validated group at 66.7% and 84.6%, O. niloticus and S. galilaeus from Sinnar, respectively. From Al Sabaloga it reclassified O. niloticus at 97.9% and S. galilaeus at 0.0% due to its small sample size. In Khashm El Girba the cross validated group reclassified O. niloticus at 100% and C. zilli at 94.4%, respectively. Comparison between the values and variables clearly reduced the overlap when 3 traits were used instead of 19 traits. Cluster analysis placed S. galilaeus from Al Sabaloga in a separate branch of the dendrogram due to its small sample size