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Background: Today, Methicillin-Resistant Staphylococcus Aureus (MRSA) has become one of the public health concerns due to its resistance to antimicrobial drugs, and this problem makes treating patients with infections caused by this bacterium difficult. Infections caused by methicillin-resistant Staphylococcus aureus (MRSA) strains are pervasive in both community and hospital settings, primarily attributable to Staphylococcus aureus' capacity to colonize areas like the nose or skin. In this study, with the aim of comparing phenotypic (disc diffusion method) and genotypic (PCR) methods, to detect methicillin-resistant Staphylococcus aureus isolated from patients of hospitals under supervision of Tehran university of medical sciences, and also detection of nor A, that is the one of the most important genes in efflux pump cluster genes. Methods: The present research was a cross- sectional study that was conducted from February 2022 to September 2023. In this research, 43 isolated strains of Staphylococcus aureus from wound discharge and blood samples, were collected from different departments of Tehran hospitals and had submitted to the research laboratory of the school of allied medical sciences in Tehran university of medical sciences. After identifying the strains, the resistance of the isolates to 14 types of antibiotics was checked by disk diffusion method. Results: Staphylococcus aureus diagnostic tests including gram staining on colonies, catalase, coagulase, DNase tests were performed and it was found that all strains were Staphylococcus aureus. In the next step, all samples were resistant to Cloxacillin by disc diffusion method, and the presence of mec A gene in them was confirmed by PCR method, thus the presence of MRSA strains was confirmed from the genotypic point of view. Of the 43 Staphylococcus aureus strains, 26 samples were identified as having the nor A gene by PCR and electrophoresis. Conclusion: The results of the present research have shown that the prevalence of Staphylococcus aureus bacteria in hospital samples is significant and resistance to methicillin and ciprofloxacin has increased in the strains of this bacteria.