Monascus spp., one of the important microbial resources both for food and medicine in China, can produce kinds of useful secondary metabolites, such as the natural food additive Monascus pigments, the cholesterol-lowering substance monacolin K and so on. Meanwhile, this genus also has the ability to secrete the mycotoxin citrinin, causing a safety risk to Monascus-related products. Therefore, how to promote the production of the useful metabolites and eliminate the production of citrinin has become a hot topic. Over the past decade, with the development and application of molecular biological approaches in Monascus spp., great efforts have been made to explore the basical knowledge about biosynthesis of secondary metabolites, and many genes involved in biosynthesis of Monascus pigments, monacolin K and citrinin have been identified and characterized. The latest achievements were summarized in this paper, in the purpose of providing potential approaches to manipulate and improve industrial Monascus strains efficiently.