Monascus pigments, which are produced by various species of Monascus, often have been used as a natural colourant and as traditional natural food additives, especially in Southern China, Japan and Southeastern Asia. The limitation of wide using Monascus pigment is attributed to one of its secondary metabolites named citrinin. The aim of this study was to investigate the influence of pigment and citrinin production via submerged fermentation (SmF) and solid-state fermentation (SF) from rice (Oryza sativa L.) by Monascus purpureus AS3.531. The optimal fermentation temperature and pH were significantly different for pigment production through different fermentation mode (35 °C, pH 5.0 for SF and 32 °C, pH 5.5 for SmF, respectively). Adding 2% (w/v) of glycerol in the medium could enhance the pigment production. On the optimized condition, although the concentration of citrinin produced by SmF (19.02 ug/g) increased more than 100 times than that by SF (0.018 ug/g), the pigment yield by SmF (7.93 U/g/g) could be comparable to that by SF (6.63 U/g/g). Those indicate us that fermentation mode seems to be the primary factor which influence the citrinin yield and secondary factor for pigment production.