There is an extremely high incidence of antimicrobial resistance of the clinical isolates of Staphylococcus aureus in Korea. This study carried out a molecular investigation to determine the prevalence of the community-associated antimicrobial-resistant S. aureus and methicillin-resistant S. aureus (MRSA). The percentage resistance from the nasal swabs of healthy volunteers in 2003 in Seoul is as follows: penicillin (91%), erythromycin (EM, 14%), gentamicin (GM, 9.3%), tetracycline (TE, 8.2%), cephalothin (4%), oxacillin (OX, MRSA; 3.8%), clindamycin (CC, 2.6%), ciprofloxacin (CIP, 0.8%), and sulfamethoxazole/trimethoprim (0.6%). The community-associated MRSA (C-MRSA) strains were examined by pulsed-field gel electrophoresis (PFGE) analysis of the SmaI macro-fragments, multilocus sequence typing (MLST), and staphylococcal cassette chromosome mec (SCCmec) typing using the PCR analysis. The Korean C-MRSA isolates were clustered into three distinct groups. One PFGE group containing the C-MRSA strains showed resistance to CC, EM, and GM, a high level (32-96 microg/ml) of resistance to methicillin, sequence type 5 (ST5), and SCCmec type II, which is the most common hospital associated-MRSA (H-MRSA) isolated in Korea. These results highlight the heterogeneous genetic background of the C-MRSA as well as the pervasiveness of the H-MRSA isolates in this community.