Objective To provide basic data for molecular tracing of foodborne Staphylococcus aureus by genotyping of isolates from airline food in Baiyun Airport during 2013-2015. Methods Foodborne Staphylococcus aureus isolates were identified through polymerase chain reaction (PCR) method targeting coagulase gene and enterotoxin genes,the enterotoxin genes included five traditional enterotoxin genes(sea, seb, sec, sed, see)and six newly discovered genes(ser, seg, seh, sei, sej, sep). Results Six Staphylococcus aureus strains isolated from airline food were separated into two genotypes and three subtypes according to coagulase gene. The traditional enterotoxin genes (including sec and sed) and the newly discovered enterotoxin genes(including ser, seg, sei and sej)were detected from two Staphylococcus aureus strains isolated from airline food. Conclusion The result of the genotyping of coagulase gene displayed the same genotypes existing in different time and different collection sites, suggesting the maximum possibility of cross contamination of Staphylococcus aureus. Six strains of Staphylococcus aureus isolated from airline food were tested for 11 enterotoxin genes, and 2 isolates contained enterotoxin gene isolated from airline food, suggesting that Staphylococcus aureus genotype was diversified, and should strengthen the detection of the new discovered toxin gene.