Red koji or red mold rice is prepared by growing a genus Monascus on steamed rice. For centuries, it has been used in Asia for the production of fermented foods including red rice wine and fermented tofu. Although red koji is an important source of various hydrolytic enzymes critical for food fermentation, information on the enzymatic properties in red koji has been limited. Hydrolytic enzymes produced by Monascus fungi may play important roles in ripening of tofuyo (Japanese fermented tofu) regarding the chemical and physical properties of the product. This review provides an introduction of red koji, its properties, and the application of hydrolytic enzymes, especially aspartic proteinases and carboxypeptidases from Monascus fungi. We also describe tofuyo and a novel fermented soybean protein food using a microbial action originating from red koji.