The increasing number of methicillin-resistant Staphylococcus aureus (MRSA) infections strains is a global health threat. Vancomycin is one of the very limited options in treating such infections. The emergence of vancomycin-resistant S. aureus (VRSA) is therefore a great concern in clinical settings. During recent years, the incidence of vancomycin-intermediate S. aureus (VISA) and vancomycin-resistant S. aureus has increased in various parts of the world, which have been identified based on criteria defined by the Clinical and Laboratory Standards Institute (CLSI). We have recently shown a high resistance rate to methicillin in S. aureus isolates from two main university hospitals in northeastern Iran. Here we expanded the study to reveal the frequency of vanA and mecA genes in the isolated MRSA strains. We selected 45 MRSA isolates, which were shown phenotypically methicilin- resistant to further genotypic investigation of the mecA and vanA genes. DNA was extracted from bacterial suspension and mecA and vanA genes were identified using PCR technique. The majority of MRSA isolates, 42 out of 45 (93%), were positive for the mecA gene. None of the MRSA isolates were positive for the vanA gene. The mecA gene is frequently circulating among phenotypically identified MRSA isolates, which confirms the phenotypically resistant strains and explains the resistance mechanism. The high frequency of circulating mecA gene highlights the need for policies to overcome the MRSA problem in clinical settings. Though none of the isolates showed vancomycin-resistance based on phenotypic tests, we also evaluated the isolates for possible vanA gene positivity and none of the isolates were shown to be positive for the vanA gene.