Two-component systems (TCSs) play important roles in the adaptation of bacteria to environmental changes and the regulation of virulence factor expression. In addition, the association of TCSs with susceptibility to antibacterial agents has been demonstrated in some bacterial species. Staphylococcus aureus, a major human pathogen that can cause serious problems due to nosocomial infections, possesses 16 TCSs. Here we report a TCS, designated BceRS (MW2 gene ID: MW2545-44), which is related to bacitracin susceptibility. We found that BceRS regulates the expression of two transporters that determine susceptibility to bacitracin. One of these, BceAB (MW2543-42), is located downstream of BceRS, while the other, VraDE (MW2620-21), is more distant. With regard to other TCSs, VraRS and Aps/GraRS are reportedly associated with susceptibility to cell wall synthesis inhibitors and cationic antibacterial agents, respectively. Therefore, S. aureus possesses at least three TCSs that are involved in mediating its resistance to antibacterial agents.