Monascus products are used as both natural colorants and food additives all over the world. However, its safety is really an issue because of the presence of citrinin, which is considered to be hepatotoxic and nephrotoxic. Therefore, the objective of the present study was to develop an approach for using a fragment of pigment-related gene pks1 to replace citrinin-activator gene ctnA. The character of citrinin antibacterial activity to Bacillus subtilis was used for primary screening of transformants based on the foundation that the inhibition zone formed around the mutant colonies with low citrinin products will become smaller. The selected mutants were then further confirmed by polymerase chain reaction and high-performance liquid chromatography methods. During all of the processes, antibiotic markers and vectors were avoided. The results showed that the citrinin products of mutants were reduced to 42%, while the pigment products were improved to 33.9%, respectively, over those of the wild-type strains.