The present study was conducted to determine morphometric characteristics of two populations (Lake Burullus and Nile) of four Tilapia species (Oreochromis aureus, Oreochromis niloticus, Sarotheodon galilaeus, and Tilapia zillii) to establish whether populations could be differentiated based on morphometric variability which may result from different habitat ecology. Thirteen morphometric characters were used to test the hypothesis differentiation. Data obtained were analyzed statistically using analysis of variance (ANOVA). The obtained results revealed a significant intra-specific variability (P < 0.05) between different collection sites in some traits, while no variability was found in other traits. In O. aureus, SL, BD, PAL and HL showed distinctive variations between collection sites. In S. galilaeus, there was variability in BD, PPL and CPL between collection sites. While in O. niloticus, SL, BD, PAL, HL and ED showed significant variations between collection sites. In T. zillii, BD, PDL, PAL, CPL, CPD, SnL were the traits that have significant variability between collection sites. Morphological variations within a species may be associated to different habitat characteristics such as water turbidity and food availability.