This study aims to investigate the antimicrobial susceptibility, molecular characteristics and virulence genes of community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) isolates with skin and soft tissue infections (SSTIs). Outpatients with SSTIs visiting five medical and health institutions were enrolled from 2011 to 2013. Available S. aureus isolates were characterized by antimicrobial susceptibility testing, and detection of PVL genes. For CA-MRSA isolates, we performed typing of staphylococcal cassette chromosome mec (SCCmec), multi locus sequence typing (MLST) and carriage of 27 virulence genes. A total of 203 S. aureus strains were isolated from 1400 outpatients with SSTIs, and 21 (10.3%) were CA-MRSA isolates. The positive rate of PVL genes among S. aureus, CA-MRSA and methicillin-susceptible S. aureus (MSSA) isolates were 39.4%, 71.4% and 35.7%, respectively. CA-MRSA strains had greater sensitivity to non-β-lactam antimicrobial agents. All CA-MRSA isolates belonged to SCCmec IV and V, accounting for 47.6% and 52.4%, respectively. ST59 was the most common lineage accounting for 76.2%; ST59-SCCmec IVa-PVL-positive clone was found to be the predominant clone, accounting for 38.1%. All CA-MRSA isolates were found to be positive for one or more virulence genes, 28.6% of isolates carried PVL, seb, sek, seq, hla, hlb, hld and hlg-2. CA-MRSA infections were relatively uncommon in outpatients with SSTIs, but they carried many virulence genes, ST59-SCCmec IV a-PVL-positive clone was the predominant clone in Wuhan, China.