To obtain an overview of epidemic characteristics of Staphylococcal enterotoxins(SEs), Panton-Valentine leukociclin(PVL), exfoliative toxins(ETs), and toxic shock syndrome toxin1(TSST-1) genes of Staphylococcus aureus(S.aureus) isolated from food and food poisoning samples in Xi’an from 2006to 2011, and to compare the difference of gene distribution and genotyping between the two kinds of isolates.MethodsThe genes of sea, seb, sec, sed, eta, etb, tsst-1and pvl were detected by multiplex PCR. The multiplex PCR assay combined the primers of sea, seb, sec and sed in one reaction and the other four primers in another. ResultsOut of 40S.aureus strains isolated from food, 17strains were detected toxin genes(42.50%). In 21strains isolated from food poisoning, 18strains were detected toxin genes(85.71%). The detection rate of toxin genes in food poisoning isolates was much higher than that in food isolates (P<0.01). Sea(25%) and eta(12.5%) were the most common genes and sea(10.00%) and sea+eta(7.50%) were the main toxin genotypes in food isolates, and etb, tsst-1genes were not detected. Sea(76.19%) and sec(28.57%) were the most common genes and sea(42.86%) and sea+sec+tsst-1(14.29%) were the main toxin genomic types in food poisoning isolates, and PVL gene were not detected.ConclusionThere were significant differences in toxin gene distribution and genotyping between S.aureus isolates from food and isolates from food poisoning.