Phenotypic variation based on both morphometric character indices and meristic counts between wild and cultured Sea bream (Sparus aurata) populations were phylogenetically analyzed aiming to identify and measure the amount of phenotypic differences and also to help assess the degree of phenotypic plasticity presented by these populations. The results revealed a significant difference (P≤0.05) in most of morphometric character indices between wild and cultured Sea bream populations. Suez Canal population presented a significant superiority in most of morphometric character indices as its individuals achieved mean values of 0.4039±0.002, 0.3829±0.002, 0.1486±0.001, 0.0879±0.002, 0.3062±0.001, 0.0948±0.001, 0.1077±0.001, 0.0761±0.001, 0.0532±0.001 and 0.0999±0.001 respectively for the indices HW/HL, BD/SL, BW/SL, CPW/SL, Dist. Pel-An/SL, Min. BD/SL, LLoDFR/SL, LLoAFR/SL, LLaAFR/SL and LSCFR/SL with a significant differences (P≤0.05) from the other populations. The hierarchical cluster analysis based on quantitative phenotype (morphometric, landmark and meristic character indices) grouped the four populations of Gilthead Sea bream (Sparus aurata) into two major category groups; Suez Canal, Bardawil and cultured populations group, and Alexandria, population group. Within these major grouping, Suez Canal, Bardawil and cultured populations were grouped close together and they were close to the major group of Alexandria population were grouped close.