Abstract:[Objective] To determine whether the byssochlamic acid (BA) gene cluster exists in the genome of Monascus ruber M7, and to explore the effect of polyketide synthase gene mr-Bys and 3-hydroxyacyl-CoA dehydrogenase gene mr-hdh in BA gene cluster on BA production. [Methods] The M7 genome was analyzed by bioinformatics methods to identify the BA candidate gene clusters. The effects of mr-Bys and mr-hdh on BA production were studied by the gene knockout and over-expression methods. BA was analyzed by ultra-performance liquid chromatography (UPLC) and mass spectrometry (MS). [Results] A BA gene cluster was found in the genome of M. ruber M7. After knocking out mr-Bys, BA disappeared, while both knockout and over-expression of mr-hdh affected BA production by M. ruber M7. [Conclusion] There is a BA gene cluster in the genome of M. ruber M7, which can produce BA. The research results enrich the research on the secondary metabolites of Monascus spp. and their synthetic pathways and lay a foundation for the development of new products using Monascus spp.