Monascus pigments (MPs), a kind of natural pigments with diverse biological activities produced in the secondary metabolism of filamentous Monascus, are widely used as colorants in food, cosmetics and health-care products in East Asia. [Objective] In this study, a PigE gene related to MPs biosynthesis in Monascus purpureus Mp-21 (strain Mp-21) was cloned and characterized.[Methods] The PigE gene (one of MPs genes) was knocked out by homologous recombination in strain Mp-21 and the biological characteristics before and after the gene deletion were analyzed with regard to phenotypes, microstructures, growth rates, MPs and citrinin.[Results] The resulting data demonstrated that the disruption of PigE mainly led to the upregulation of yellow pigments in varieties and yields. In comparison to an MPs complex mixture in which the red pigments were dominant in the wild-type strain Mp-21, the △PigE (a PigE gene deletion mutant) lost the ability to produce red pigments and produced at least five new yellow pigments. The MPs production was up to 3548.2 U/g and about 4.82-fold as that in the wild type strain Mp-21 after liquid-state fermentation for 13 d. Additionally, the citrinin production had no significant change, while the productive period was delayed on account of a longer period to adapt to the growing condition. The deletion of PigE blocked the transformation pathway of the yellow pigments to orange pigments, which made the △PigE more favorable to form yellow pigments. As the formation of red pigments required more complex conditions such as amino acids and suitable pH in culture medium, the △PigE prefers to synthesize yellow pigments first and lost the ability to produce red pigments. [Conclusion] This study provides a possible way for the construction of genetic engineering Monascus strains with high yield of yellow pigments.