Abstract: Genetic relatedness was estimated among five populations of the European sea bass (Dicentrachus labrax L.) using 9 RAPD (Randomly Amplified Polymorphic DNA) primers. Samples were collected from Egyptian coast Mediterranean (Al Borge, Meadea and Rashid) and other two populations were from Manzalla lake and Bardawil lagoon. These primers produced 94 bands that could be scored with high confidence. On average, each primer gave rise to 6-16 bands and a majority of the bands was polymorphic. The percentage of polymorphic bands in Al-Borge (45%) and Meadea (44%) populations was low compared to Rashid (55%) and Manzalla (52%) populations. RAPD analysis showed that the Bardawil population had higher genetic polymorphism (64%) than the other populations. The phylogenetic tree constructed by unweighted pair-group method of analysis (UPGMA) shows the Al-Borge and Manzalla populations and Meadea and Rashid populations, respectively, seems to be approximately as closely linked to each other from the dendrogram. The Bardawill population is more related to the Rashid and Manzalla populations. High levels of genetic variation and population differentiation indicated dynamic evolution in these populations as revealed by variation at RAPD loci.