We studied the genetic structure at six microsatellite loci of the Mediterranean sea bass (Dicentrarchus labrax) on 19 samples collected from different localities in the western and eastern Mediterranean basins. Significant divergence was found between the two basins. The distance tree showed two separate clusters of populations which matched well with geography, with the noticeable exception of one Egyptian sample which grouped within the western clade, a fact attributable to the introduction of aquaculture broodstock. No heterogeneity was observed within the western basin (theta = 0.0014 and n.s.). However, a significant level of differentiation was found among samples of the eastern Mediterranean (theta = 0.026 and p < 0.001). These results match with water currents but probably not with the dispersal abilities of this fish species. We thus hypothesize that selective forces are at play which limit long-range dispersal, a fact to be taken into account in the debate about speciation processes in the marine environment.