The antimicrobial effect of the methanol extract of Inula britannica flowers against methicillin resistant Staphylococcus aureus (MRSA) was investigated. It was confirmed that the methanol extract is mainly composed of quercetin, which has antimicrobial properties. The antimicrobial effect of the methanol extract against 3 MRSA strains was determined by the disc diffusion method. The minimal inhibitory concentrations were ranged from 0.625 mg/ml to 1.25 mg/ml, and the minimum bactericidal concentrations were 2.5 mg/ml. Time kill kinetics revealed bactericidal activities, and the morphological alterations in S. aureus ATCC 33591 treated with the extract were observed using a scanning electron microscope. The methanol extract affected the expression of the resistant genes, mecA, mecI, and mecRI in mRNA. Therefore, the methanol extract of I. britannica flowers clearly demonstrated an antimicrobial effect against MRSA and these results suggest a potential for application as a natural antimicrobial agent.