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More and more people pay attention to citrinin produced by Monascus, which has nephrotoxic activity in mammals. It was reported that pksCT gene is responsible for citrinin biosynthesis in Monascus purpureus. In this paper, two DNA fragments in both ends of pksCT were amplified by genomic PCR from fourteen Monascus spp. strains. The PCR products were gained from all of the strains. It is suggested that pksCT gene was highly conserved in different citrinin-producing Monascus strains. A pksCT-replacement vector (pHD106) was constructed to disrupt pksCT with a hygromycin resistance gene as the selection marker, and was transformed into M. aurantiacus Li AS3.4384. Three transformants (M. aurantiacus PHDS18, PHDS26, PHDS31) were selected from transformant selective plates. The targeting fragment D was gained by genomic PCR from PHDS18 and PHDS26 except PHDS31. The expressing citrinin capacities of PHDS26 was decreased by about 98%, while PHDS18 was reserved the high capacity of producing citrinin, after 10 days of growth on YM medium. The results indicated that PHDS26 is a pksCT-disrupted strain. There are maybe other genes besides pksCT responsible for citrinin biosynthesis in M. aurantiacus. It is the effective way to solve the problem of citrinin in M. aurantiacus products by constructing replacement vectors to disrupt the genes responsible for citrinin biosynthesis to reduce the capacity of expressing citrinin.