Abstract: Objective To investigate the enterotoxin genes distribution and molecular characteristics of Staphylococcus aureus isolated from patients in Ningbo. Methods S. aureus strains were collected from the patients. S. aureus enterotoxin gene A(sea), S. aureus enterotoxin gene B(seb), S. aureus enterotoxin gene C(sec)and S. aureus enterotoxin gene D(sed)were detected with polymerase chain reaction (PCR). Molecular subtyping were conducted with multi-locus sequence typing (MLST). Results A total 155 clinical strains were collected in 2006,2008 and during 2011-2013, in which 45 were enterotoxin gene positive. The positive rates of 4 enterotoxin genes were 16.77%, 5.81%, 11.61% and 3.87% respectively. The 45 strains formed 8 kinds of assortment of genes. Sea (14 strains), sec (9 strains) and the combination of sea and sec (8 strains) were predominant. The 45 strains could be divided into 15 sequence types (STs) with MLST. ST12, ST573 and ST1121 were newly found in Ningbo compared with other areas of China. ST1 (14 strains), ST5 (6 strains), ST1121 (4 strains) and ST15 (4 strains) were the major STs. The positive rate of 4 STs was 62.22%. The phylogenetic tree had 7 branches. The positive rate of sea and sec genes were 72.73% and 54.55% in ST1 clone complex. The combination of sea and sec was the major genes in ST1 clone. Conclusion The positive rate of enterotoxin gene was high in S. aureus isolated from the patients in Ningbo. Most of the clinical strains carried sea and sec genes. There were 15 STs circulating in Ningbo. ST12, ST573 and ST1121 were newly found in clinical strains isolated in Ningbo. ST1 clone complex was the predomiant genotype, followed by ST5 clone complex. Most of the ST1 clone complex carried sea and sec genes.