Monacolin K (MK) produced by Monascus spp. is mostly used to regulate cholesterol level, while it can be contaminated by citrinin, a mycotoxin yielded by some Monascus strains. To develop production of citrinin-free MK, an M. sp. MS-1 strain, identified as M. pilosus by morphologies and internal transcribed spacer sequences analysis, was isolated from red fermented rice. After 14 days of fermentation, yields of citrinin-free MK could be up to 0.58 mg/mL and 16.45 mg/g in liquid- and solidstate fermentation products under optimal conditions, respectively. Further determination revealed that no citrinin biosynthesis related genes such as ctnA, pksCT, ctnE, and ctnR were detected. Thus, HPLC combined with citrinin-related gene analyses can be used for rapid screening of non-citrinin production Monascus strains.