Objectives: Molecular typing such as spa typing is used to control and prevent of Staphylococcus. aureus widespread in hospitals and community acquired. Hence, the aim of this study was to find the common types of S. aureus strains circulating in Shiraz via spa and SCCmec typing methods. Results: Total of 159 S. aureus isolates were collected from two tertiary hospitals in Shiraz. Isolates were identified by biochemical tests. Antimicrobial susceptibility tests were performed by standard disk diffusion method and then genetic analysis of bacteria was performed using SCCmec and spa typing. In this study 31.4% of the isolates were methicillin-resistant S. aureus. The majority of isolates were SSC mec type ІІІ. Spa type t030 was the most prominent type among MRSA strains. In this study, for the first time in Iran, spa003, t386, t1877, t314, t186, t1816, t304, t325, t345 were reported. It was shown that there is a possibility that these spa types are natives to this region. Our findings showed that SCCmec ІІ, ІІІ and IV disseminate from hospital to community and vice versa. Thus, effective monitoring of MRSA in hospital and community is desirable. Keyword: Staphylococcus aureus , methicillin-resistant S. aureus (MRSA), SCCmec typing, spa typing