Abstract: The aim of this study was to understand the correlation between the key genes responsible for citrinin biosynthesis in the strain and the citrinin content in Hongqu. In this study,6 pairs of primers targeting the key genes responsible for citrinin biosynthesis were designed to amplify the corresponding region with genomic DNA of 25 different Monascus strains collected from various Hongqu products as templates. Simultaneously,the traditional production process was used to prepare Hongqu. The citrinin of these Hongqu purified by immuno-affinity columns was subjected to UPLC detection. The results showed an obvious consistency between the PCR amplification and UPLC detection. When the PCR amplification was positive targeting key genes responsible for citrinin synthesis,the citrinin content of Hongqu fermented by the described Monascus strains exceeded 50 μg/kg(the limit standard for citrinin in functional Hongqu,stated in QB/T 2847-2007);while the key genes of citrinin synthesis was negative by PCR amplification,the citrinin content was lower than the instrumental detection limit(15.92 μg/kg),which was much lower than the citrinin limit standard stated in QB/T2847-2007. These results suggested that the PCR method in this study not only could be used to judge whether citrinin in Hongqu produced by traditional process exceeded the limit of the standard stated by QB/T 2847-2007,also provided basic information for evaluating the ability of different strains to secret citrinin.