Microsatellite markers were used to investigate the genetic structure of the two most important cultured fish in the Mediterranean Sea, the gilthead seabream (Sparus aurata) and the European seabass (Dicentrarchus labrax), from two (one wild and one farmed) populations in Western Mediterranean (Spain) and from two (one wild and one farmed) populations Eastern Mediterranean (Greece). All populations were in Hardy-Weinberg disequilibrium. Interestingly, wild and farmed populations for both species from Greece were genetically differentiated and could be distinguished from each other. We used Bayesian methods for cluster analysis of farmed and wild populations. Our analysis has implications for the identification of escapees from fish farms to the wild.