Red yeast rice is made by growing Monascus on rice. Red yeast rice is used as a food all over the world. In recent years, red yeast rice has been increasingly used not only as a natural coloring agent, but also as a functional food with effects such as lowering blood pressure and lowering cholesterol. Monascus produces monacolin K and azaphilone pigments that affect human health, but it also produces citrinin, a mycotoxin believed to be harmful to health. Therefore, it is necessary to develop Monascus that does not produce the citrinin and can be used safely and securely as food. We conducted genome analyses of three Monascus strains using a next-generation sequencer and secondary metabolite analyses using LCMS. As a result, we found Monascus pilosus NBRC4520 and Monascus ruber NBRC4483 that do not produce the citrinin at the genome and LCMS analysis levels. Although Monascus ruber has been reported to produce citrinin from previous research reports, Monascus pilosus has been reported that biosynthetic genes for citrinin are not conserved in several strains at the genome level. Therefore, Monascus pilosus is considered the safest Monascus strain for use as food. Our goal is to contribute to the health of people around the world by studying safe and reliable Monascus for use in food.