Resistant strains of Staphylococcus aureus have now been described globally, as significant pathogens, particularly associated with skin and soft tissue infections, including abscesses, cellulitis and furunculosis. Novel antimicrobial products and new methods to combat this problem are urgently needed. Pepper has been used since ancient times not only for increasing the flavor of foods, but for its preservation and medical properties. This study was designed to assess the antibacterial activity of ethanolic extract of two pepper species, Capsicum annuum and Capsicum frutescens, against clinical strains of antibiotic-resistant Staphylococcus aureus. After the isolation of 56 strains of S. aureus from nosopharyngial of hospitalized patients, antibiotical resistance of them was determined by Kirby-Bauer method. Then fourteen multidrug-resistant strains were selected and antibacterial effects of the ethanolic extracts of two Capsicum species were evaluated by disc-diffusion method. Results showed that both extracts were effective on most of the bacteria, but Capsicum frutescens extract had approximately higher inhibition than Capsicum annuum extract, with maximum inhibition zone 12mm against strain of S. aureus that was resistant to four antibiotics including Cefixime, Tetracycline, Methicillin and Oxacillin. This study shows that peppers, like antibiotics or even better than them, have an antibacterial activity against the tested microorganisms. Also the results obtained from this study support the idea of proposing the use of Capsicum extracts as a natural antibacterial agent in the treatment of infected diseases and other diseases that are insensitive to drugs.