In this study, protein hydrolysate was produced from the wastes resulting from the filling of culture sea bream (Sparus aurata) and sea bass (Dicentrarchus labrax). Hydrolysates were developed by employing the alcalase and flavor enzyme. In addition, the functional properties of hydrolysates were characterized such as emulsion, color, rage and antioxidant as well as amino acid compositions. Also, the effects of storage time on the hydrolysates which was developed by using the two different enzymes and stored at 18°C on 6 months were determined. As a result, it was found that hydrolysate protein powder made by alcalase was showed higher level of functional and antioxidant properties compared to the flavor enzyme.