The purpose of the present invention is to provide an agent for improving intestinal flora which can increase the number of beneficial bacteria such as lactic acid bacteria and Bifidobacterium to improve intestinal flora by using an enzyme. A protease consisting of a polypeptide having an amino acid sequence shown in SEQ ID NO: 1 can increase beneficial bacteria such as lactic acid bacteria and Bifidobacterium in intestines to exert an excellent effect of improving intestinal flora.