ABSTRACT Staphylococcus aureus is an important human pathogen and vancomycin is widely used for the treatment of S. aureus infections. The global regulator agr is known as a well-described virulence regulator. Previous studies have found that agr -dysfunction strains are more likely to develop into vancomycin-resistant strains, but the mechanism for this phenomenon remains unknown. VraSR is a two-component regulatory system related to vancomycin resistance. In this study, we found that the expression levels of vraR were higher in agr -dysfunction clinical strains than in the agr -functional strains. We knocked out agr in a clinical strain, and quantitative reverse transcription PCR and β-galactosidase activity assays revealed that agr repressed transcription of vraR . After vancomycin exposures, population analysis revealed larger subpopulations displaying reduced susceptibility in agr knockout strain compared with wild-type strain, and this pattern was also observed in agr -dysfunction clinical strains compared with the agr -functional strains. Electrophoretic mobility experiment demonstrated binding of purified AgrA to the promoter region of vraR . In conclusion, our results indicated that the loss of agr function in S. aureus may contribute to the evolution of reduced vancomycin susceptibility through the downregulation of vraSR .