Objective Analysis of the antimicrobial resistance characteristics， molecular characteristics， and homology of Staphylococcus aureus， the source of two cases of food poisoning in Nan’an District， Chongqing Municipality.Methods Pathogens were isolated and identified from anal swabs of cases and practitioners， samples of the food processing environment and retained food. The isolates were subjected to enterotoxin detection， virulence gene detection（qPCR）， antimicrobial susceptibility testing， and whole genome sequencing was performed to obtain virulence and resistance genes carried by the isolates and to perform multilocus sequence typing and single nucleotide polymorphism analysis.Results Ten S. aureus strains were isolated from anal swabs of eight cases， one environmental sample， and one retained food sample， of which four and six strains were isolated from A and B incidents， respectively. In the same incident， S. aureus produced the same enterotoxin with the same resistance profile. Using the qPCR method， the virulence genes of the S.aureus strains producing SEA and SEE were identified； the results showed that sea， seb， sec， and sed were positive. Using the gene annotation technique， the S.aureus producing SEA and SEE were discovered to have the virulence gene sea. By using qPCR and gene annotation approaches， it was demonstrated that the virulence genes sea and seb were positive for strains producing SEA， SEB， and SEE. the resistance profiles were PEN-ERY and PEN respectively. The isolates with resistance profiles PEN-ERY， all carried the associated resistance genes blaZ and erm（A）except for one isolate that did not carry the associated resistance gene blaZ， whereas the isolates with resistance profiles PEN all carried the associated resistance gene blaZ. The plasmid replicons carried by the isolates were mainly rep16， rep19， rep5a. MLST analysis showed 100% homozygosity for the same incident， and MLST typing of S. aureus for the two incidents was ST30 type and ST59 type respectively. Single nucleotide polymorphism analysis of the same incident was highly homologous.Conclusion Therefore， these two events were both food poisoning events caused by S. aureus contamination. it is necessary to further strengthen the education and management of restaurants. S. aureus strains were resistant to penicillin. Based on whole genome sequencing， multilocus sequence typing and single nucleotide polymorphism analysis of the strains can be used for homology analysis of aggregation incidents caused by S. aureus.