The development of marine aquaculture systems has raised concerns about the impact that intentional (restocking) or unintentional (escapes) releases may have on natural populations. On this regard the genetic integrity of wild populations is threatened by: 1) biological invasions, 2) loss of genetic variation, 3) change of genetic architecture, and 4) loss of local adaptation. My study concerns the genetic characterization of both wild populations and (un)intentionally introduced populations as recommended by the Code of Conduct for Responsible Fisheries. This aim has been pursued focusing on three main issues. The first, on the gilthead sea bream, highlighted that farmed populations were genetically divergent from wild ones. The other two issues are related to restocking of potentially exploited natural stocks. To this end we investigated the Mediterranean basin-scale genetic structure of the grooved carpet shell; our results evidenced an overall lack of genetic structure throughout the western Mediterranean which may be used in planning future management of this natural resource. In addition, we analysed also populations of its allochthonous counterpart, the manila clam, that show relatively high levels of genetic variation suggesting that this species may cause problem to grooved carpet shell. With regard to the grey flathead mullet, results show levels of genetic differentiation as small as 1% and suggested the occurrence of a unique genetic stock along Sardinian coasts.