Although many antibiotics are available for the treatment of bacterial infections, the emergence and global spread of antibiotic-resistant bacteria is a community-wide problem. To overcome this problem, we must explore alternative antimicrobials. This study investigated the antibacterial properties of quercetin, a flavonoid present in vegetables and fruits. Quercetin was tested against gram-positive and gram-negative bacteria and was found to exert selective antibacterial activity against Staphylococcus aureus, including methicillin-resistant S. aureus (MRSA), and Staphylococcus epidermidis. Some clinical MRSA strains showed remarkable susceptibility to quercetin. In combination with antibiotics, such as oxacillin, ampicillin, vancomycin, gentamicin, and erythromycin, quercetin showed markedly enhanced antibacterial activity against MRSA. We also report quercetin-induced aggregation of S. aureus cells; the morphological changes in these cells, as assessed by electron microscopy; and the colony-spreading ability of quercetin-sensitive MRSA, all of which revealed the unique antibacterial properties of quercetin against S. aureus.