Stock identification aims to identify the subpopulations and several techniques may be used to this end. The aim of this study was to analyze and compare genetically between wild and cultured populations of sea bream using Microsatellite marker. 100 individuals from both sexes were randomly collected from 3 wild populations and one cultured population. The number of amplified bands detected varied, depending on the primers and population. The highest interpopulation genetic similarity (91%) exhibited between culture and Bardawil population and also between Bardawil and Suez Canal. While, the lowest genetic similarity (80%) was recorded between Alexandria and Suez Canal populations. Differences in genotype reflected the same amount of differences in phenotype among the studied populations. Phenotypic differences between populations can be taken as evidence of genetic differentiation. Finally, each of phenotypic or genotypic analysis can be used to classify fish populations with the same results up to the intraspecific level, or both of them can be used to assess the degree of phenotypic plasticity shown by populations