Background: Methicillin-resistant Staphylococcus aureus (MRSA) has been known as one of the most important nosocomial pathogens that able to produce a variety of virulence factors. Objectives: In this study, we aimed to describe the prevalence, presence of different virulence factors, staphylococcal cassette chromosome mec (SCCmec) and prophage typing of MRSA strains isolated from a referral hospital in Tehran, Iran. Materials and Methods: A total of 279 S. aureus strains were collected from a referral hospital in Tehran during August to December of 2013. All isolates were confirmed using species specific primers and were tested for susceptibility to oxacillin and cefoxitin disks by the recommendations of clinical and laboratory standards institute (CLSI). The staphylococcal enterotoxin (sea-seq) and pvl, hlb and sak genes were detected and typed using prophage typing and SCCmec typing methods. Results: Out of the 279 S. aureus isolates, 91 (32.6%) strains were confirmed as MRSA. Totally, 6 enterotoxin and 2 virulence factor genes were detected in MRSA strains. The sea, sek, seq and hlb genes were present in all MRSA and sak, seg, sei and sel were detected in 85%, 35%, 23% and 44% of the strains. Only SCCmec type III and type 3 ccr and 2 different prophage patterns were identified among the strains. Conclusions: Our results show the presence of clonal groups of enterotoxin-producing MRSA strains in this hospital in Tehran. The presence of bacteriophage encoded virulence factors and resistance to oxacillin enable bacteria to produce a broad spectrum range of diseases.