Abstract Background and purpose: Staphylococcus aureus is one of the major causes of community and hospital-acquired infections. Aminoglycosides are potent bactericidal agents that are often used in combination with beta-lactam or glycopeptide in treatment of staphylococcal infections. The aim of this study was to investigate the prevalence of the aminoglycoside modifying enzyme aac(6΄)-Ie/aph(2”) genes and mecA. Materials and methods: In current study, 174 clinical isolates of MRSA from different clinical specimens were tested for antibiotic susceptibility using the Kirby Bauer method. MRSA isolates were detected by disc diffusion method using 1 ug oxacillin and 30 ug cefoxitin discs. Then, MRSA strains were further analyzed for detection of mecA and aminoglycoside resistant aac (6΄)-Ie/aph (2˝) genes by PCR. Results: All strains were resistant to oxacillin and cefoxitin. The highest and lowest resistances were found against erythromycin (85.1%) and trimethoprim/sulfamethoxazole (24.7%), respectively. In PCR, mecA gene was detected in 100% of the strains and 77% of the strains were found to harbor aac(6′)/aph(2//)-Ia gene. Conclusion: According to this study, the prevalence of aminoglycosides resistant genes is increasing in MRSA isolates.