An object of the present invention is to provide an intestinal flora improving agent that can improve the intestinal flora by increasing the number of good bacteria such as lactic acid bacteria and bifidobacteria using an enzyme. The protease comprising the polypeptide having the amino acid sequence shown in SEQ ID NO: 1 can increase the number of good bacteria such as lactic acid bacteria and bifidobacteria in the intestine, and can have an excellent intestinal flora improving effect.本発明の目的は、酵素を使用して、乳酸菌やビフィズス菌等の善玉菌の菌数を増加させ、腸内菌叢を改善できる腸内菌叢改善剤を提供することである。配列番号1に示すアミノ酸配列のポリペプチドからなるプロテアーゼには、腸内で乳酸菌やビフィズス菌等の善玉菌の菌数を増加させ、優れた腸内菌叢改善効果を奏し得る。