Staphylococcus aureus is one of the important foodborne pathogens that caused food poisoning worldwide. There are several serologically distinct staphylococcal enterotoxins (A, B, C, D, E). SEC is subdivided into SEC1, SEC2, SEC3 based on their minor epitopes. Besides the enterotoxins, there are over thirty categories of extracellular proteins and toxins secreted by S. aureus, including coagulase, hemolysins, nuclease, and protein A. Among which, coagulase and protein A are critical biochemical characteristics of S. aureus. Total of 229 S. aureus strains were collected from 36 food poisoning outbreaks occurred in the Taiwan area and only ten SEC isolates were identified. Subtyping of these strains was analyzed by the polymorphism of the SEC, coagulase and protein A genes performed by polymerase chain reaction (PCR). Three strains belonged to SEC2 and seven belonged to SEC3 and PCR of the sec gene also showed to have subtypes. Two types of coagulase gene were detected by PCR and PCR-RFLP methods. Typing for the protein A gene by PCR revealed that the amplified, products digested by Hind III or not, were identical. These rapid subtyping methods developed in this study would be valuable in analyzing the sources of contaminated food in the poisoning outbreaks.