Objective To obtain an overview of distribution of enterotoxin genes and epidemic characteristics of S.aureus through gene testing and genotyping of isolates from food in Shanghai from 2006 to 2009.Methods Enterotoxin genes in 49 S.aureus strains from food were tested by PCR including five traditional enterotoxin genes(SEA-SEE) and four newly discovered genes(SEG-SEJ).Pulse-field gel electrophoresis(PFGE) was used for genotyping.Results The total detection rate of enterotoxin genes was 38.8%.And the traditional enterotoxin genes SEA and SEC were detected,93.8% of which belonged to SEC.The newly discovered enterotoxin genes including SEG,SEI,SEJ and SEH were also detected.The method of PFGE successfully classified 44 isolates into 28 gene types with 5 isolates indeterminable.Conclusion A wide varity of S.aureus genomic types could contaminate food and lead to food poisoning.The surveillance and ongoing monitoring of S.aureus should be strengthened to provide scientific basis for food poisoning prevention and control.