Objective In order to regulate the production of citrinin from the gene level and to provide a theoretical basis for improving the safety of Monascus used in food production, the quantitative analysis of citrinin in three strains of Monascus was performed, and the related gene clusters were studied. Methods The quantitative analysis of citrinin in three strains of Monascus during liquid fermentation was analyzed by high performance liquid chromatography (HPLC). The citrinin gene clusters were sequenced at Novogene Corporation (Beijing, China) and expression levels of genes involved in citrinin gene cluster were analyzed by real time polymerase chain reaction ( RT-PCR). Results There was no significant difference in the growth of Monascus purpureus YY-1, M2 and Monascus pilosus FJ-1 in both solid-state culture and liquid fermentation. In the liquid fermentation process, the yield of citrinin in M2 was the highest, followed by YY-1, and the production of citrinin in FJ-1 was the lowest. The similarity of the citrinin synthesis gene clusters in YY-1, M2 and FJ-1 reached 99.9%, exhibiting high conservation on gene level. The expression levels of six genes including membrane transport protein gene (orf5), polyketide synthetase gene (pksCT), oxidoreductase gene(ctnB), transcriptional regulation protein gene (ctnA) and dehydrogenase genes (orf1, ctnE) in the gene cluster were the highest in M2 and the lowest in FJ-1. Conclusion The citrinin yield was not related to the gene composition of citrinin synthesis gene cluster, but related to gene expression levels.