To understand enterotoxin genes distribution and molecular characteristics of foodborne Staphylococcus aureus isolated from Ningbo.Methods Enterotoxin gene A,B,C and D were detected by polymerase chain reaction (PCR). Molecular characteristics were acquired by multi-locus sequence typing (MLST).Results 190 strains of foodborne S.aureus were isolated during 2005-2012.41 strains were positive for enterotoxin gene. The positive rate of 4 enterotoxin genes were 7.37%, 5.26%, 8.95% and 5.79%, respectively. 13 strains harbored at least two enterotoxin genes. 41 strains could be divided into 9 kinds of enterotoxin gene spectrum and 12 sequence types (STs) by MLST. ST5, ST6, ST188 and ST1 were the major STs. The positive rate of 4 STs was 75.61%. Four branches were formed in the phylogenetic tree.Conclusion The positive rate of enterotoxin gene was relatively high in foodborne S.aureus during 2005-2012, and monitoring needed to be strengthened. There were significant difference in molecular typing between the strains with enterotoxin gene in Ningbo and those food isolates from other part of China.