Aims:  To investigate the molecular epidemiological study of Staphylococcus aureus from staphylococcal food poisoning (SFP) incidents in South Korea. Methods and Results:  Three hundred and thirty‐two strains isolated from ten provinces between June 1999 and January 2002 were characterized by staphylococcal enterotoxin genes, toxic shock syndrome toxin 1 (tst) gene, and exfoliative toxin genes. Toxin genotypes were sea‐seh (n = 197), sea (n = 51), sea‐seg‐sei (n = 14), seg‐sei (n = 10), seb (n = 10), seb‐sed‐seg‐sei‐sej (n = 3), sea‐seg‐seh‐sei (n = 1), sea‐seb (n = 1), sea‐sec (n = 1), seg‐sei plus eta (n = 4), and sea‐seg‐sei plus tst (n = 40). Most of the strains could be classified into three clusters of pulsed‐field gel electrophoresis (PFGE) types A and B with coagulase type VII and type E with coagulase type IV. Of the ten sequence types (ST), ST1, ST59, and ST30 were frequently showed by multilocus sequence typing. Conclusions:  The strain belonging to PFGE pattern A with sea‐seh gene, coagulase VII, and ST1 was the most epidemic clone of SFP incidents in Korea.