Background and objective: Meticillin resistant Staphylococcus aureus (MRSA) now is well documented as a nosocomial pathogen causing a variety of infections in human. Aminoglycosides are a class of bactericidal antibiotics which play an important role in treatment of staphylococcal infections. The aim of this study was to illustrate the phenotypic and genotypic resistance to aminoglycosides among MRSA strains isolated from 2 hospitals in Tehran, during 2011 and 2012.Materials and methods: During a year, a total of 575 strains of S. aureus were collected and analyzed further. Resistance of strains to ozacillin and cefoxitin was determined using disk diffusion method in accordance with guidelines of CLSI. MRSA strains were collected and susceptibility of strains to 15 different antibiotics was determined. Minimum inhibitory concentrations (MICs) of oxacillin, vancomycin and gentamicin were evaluated using broth microdilution assay, and presence of mecA and pvl gene was showed by PCR method. For SCCmec and ccr typing, multiplex-PCR assays were employed and the genes encoding aminoglycoside modifying enzymes were detected.Results: In this study, 127 strains were resistant to oxacillin and cefoxitin and also harbored mecA gene. The highest resistance was to penicillin (100%), erythromycin (91%), ciprofloxacin (90%), kanamycin (86%), tobramycin (84%) and clindamycin (81%) and also, 60% of strains were gentamicin resistant. On the other hand, all isolates showed susceptibility to vancomycin, linezolid and quinupristin-dalfopristin. Thirty six and 32% of MRSA strains were resistant to high level of oxacilin and gentamicin (MIC³512mg/ml). SCCmec type III and type 3 ccr were the dominant types among MRSA strains. the frequency of aac (6’)-Ie+aph (2’), ant(6)-Ia, ant (4’)-Ia and aph (3')-IIIa, were detected successfully in 77%, 55%, 50% and 26% of strains. Moreover, the presence of pvl gene was limited to community acquired MRSA strains.Conclusion: Our findings illustrated the presence of aminoglycoside resistant strains of MRSA in hospitals in Tehran. These strains also showed high level resistance to other antibiotics and harbored SCCmec type III, indicating their hospital origin. Moreover, emergence of MRSA strains with high susceptibility to all classes of antibiotics, except for penicillin, are able to acquire antibiotic resistance genes, is an urgent for public health.