Serrapeptase is a kind of alkaline protease from Serratia marcescens. Due to its excellent anti-inflammatory and anti-swelling function, serrapeptase has been applied to treat some diseases in clinical for many years. In order to obtain strains with the characteristics of fine hereditary stability and prodigiosin negative for high-yield production of serrapeptase, a strain isolated from the intestine of silkworm (Bombyx mori), S. marcescens LL-413 was mutated by ultraviolet and microwave continuously. As results, 2 strains, designated as MW-9 and MW-14, were selected out. Their productivity of serrapeptase was 982 U/mL and 956 U/mL, which respectively was 1.98 and 1.92 times higher than that of the original strain.