Skin and soft tissue infections (SSTI) are a common infection among both outpatients and inpatients. The most frequently isolated bacterium in SSTI was Staphylococcus aureus, a quarter of which was methicillin‐resistant S. aureus (MRSA). In this study, to investigate molecular epidemiology of the 141 MRSA strains collected in the Japanese nationwide surveillance, we performed multiplex real‐time polymerase chain reaction to detect staphylococcal cassette chromosome mec (SCCmec) type and virulence genes. The percentage of SCCmec types I, II, III and IV was 1.4%, 52.5%, 5.7% and 40.4%, respectively. According to the SCCmec type, we classified the strains into health‐care‐associated (HA)‐MRSA (n = 84) and community‐associated (CA)‐MRSA (n = 57). Among the virulence genes, the percentage of enterotoxin C gene‐positive strains was significantly higher in CA‐MRSA than in HA‐MRSA. No significant differences were detected between the two groups in terms of antibiotic susceptibility and patients’ background information, classification of SSTI or symptoms of SSTI.