Yellow Monascus pigments were prepared from fermentation broth after extractive fermentation in nonionic surfactant micelle aqueous solution. First, Monascus pigments were transferred from nonionic surfactant micelle aqueous solution into ionic liquid phase by ionic liquid based microemulsion extraction, in which the recovery yield of yellow Monascus pigments based on absorbance at 410 nm reached to 95.5%. Then, the yellow Monascus pigments in the ionic liquid phase were recovered by ionic liquid-butanol two-phase extraction, in which the recovery yield of yellow Monascus pigments reached to approximately 95%. Further purification of yellow Monascus pigments was demonstrated by removal of orange Monascus pigments via selective aminophilic reaction between orange Monascus pigments and MSG (monosodium glutamate). The results indicated that there was no aminophilic reaction between yellow Monascus pigments and primary amines by replacement of 4-H-pyran cycle in orange Monascus pigments with 2-H-pyran cycle in yellow Monascus pigments. This fundamental fact provides a novel strategy for removal of orange Monascus pigments from yellow ones. It also sheds light on why orange Monascus pigments but yellow ones exhibit strong cytotoxicity. (C) 2015 Elsevier B.V. All rights reserved.