To evaluate the epidemiology and molecular features of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) and methicillin-sensitive S. aureus (MSSA) from children with skin and soft tissue infections (SSTIs) in Beijing, China, prospective community-acquired S. aureus SSTIs surveillance was conducted at the Beijing Children's Hospital, Beijing, China, for a 12-month period from August 1, 2008, to July 30, 2009. Susceptibility to 12 antimicrobials was determined by the agar dilution method. Genotypic characteristics of CA-MRSA isolates were tested by SCCmec typing, spa typing, and multilocus sequence typing. Panton-Valentine leukocidin gene was detected. Of 1104 cases, 31.8% (351) were community-acquired S. aureus. CA-MRSA accounted for 4% (14) of S. aureus. Among 14 CA-MRSA and 120 MSSA isolates tested, 100% and 91.7% were multidrug resistant, respectively. ST59-MRSA-IVa-t437 (42.9%) was the most common form of CA-MRSA. Spa typing analysis of 120 MSSA isolates was performed, followed by pulsed-field gel electrophoresis and multilocus sequence typing of a selected number of isolates. The most common spa types among MSSA were t084 (8.3%), t091 (5.8%), t034 (5%), t127 (4.2%), t002 (4.2%), and t796 (4.2%). No predominant spa type was seen. Of the MSSA isolates that could be classified into spa-CCs, 15.0% had a genetic background observed in CA-MRSA clones (spa-CC437, spa-CC342, and spa-CC377). Panton-Valentine Leukocidin (PVL)-positive community-acquired S. aureus strains were more commonly associated with skin abscesses than other SSTIs (29.4% versus 5.9%, P < 0.01).In conclusion, CA-MRSA infections are not common among Chinese children with SSTIs. Our findings show that MSSA strains in China have diverse genetic backgrounds.