In the present study, protein of muscles of commercially important marine fishes Nemipterus japonicus and Exocoetus volitans were extracted by trypsin and their hydrolysis conditions viz., temperature, time, and enzyme to substrate concentration on degree of hydrolysis were studied by response surface methodology. The optimum values for N. japonicus was found as temperature, 30°C, hydrolysis time of 100 min an enzyme/substrate concentration of 1.59% whereas, for E. volitans muscle protein, optimum hydrolysis conditions were temperature, 30°C, hydrolysis time of 115 min and enzyme/substrate concentration of 1.67%. Furthermore, amino acid sequence of antioxidant peptides derived after chromatographic purification was identified by ESI-MS/MS. The analysis of peptides showed sequences as Glu-Ser-Asp-Arg-Pro (620.3 Da) and Gly-Trp-Met-Gly-Cys-Trp (747.3) for N. japonicus and E. volitans muscle, respectively. The peptides contained important antioxidant amino acids and acted as good antioxidant peptides to scavenge free radicals.