Monascus spp., a kind of filamentous fungi, produce abundant of important metabolites which were widely used in the fields of food and medicine. Until now, there are few reports on the important functional genes of the Monascus spp. due to little genetic information. In this paper, the feasibility of gene deletion mediated via Agrobacterium tumefaciens on the basis of homologous recombination was analyzed by studying on the deletion of the RGS domain of putative G-protein signaling regulator gene mrfA in Monascus ruber. The length of homologous arms of deletion vector pC805S were 958 bp and 824 bp, respectively. There were 26 transformants in which homologous recombination occurred in 138 transformants and the recombination rate was 18.8%. The result showed it was feasible to identify the function of unknown gene in M. ruber with the targeted-deletion technology mediated via A. tumefaciens.