Objective To compare four PCR genotyping method for Clostridium botulinum, and provide the reliable method for detection and identification of Clostridium botulinum from surveillance and foodborn poisoning in Sichuan Province. Methods Six strains of C.botulinum types A, B and E were used to compare four PCR genotyping method —one multiplex PCR method was from US FDA, two multiplex PCR method and one real-time PCR method were from ISO, and the differences were preliminarily analyzed. Results Three multiplex PCR method could detect C.botulinum types A, B and E in a single reaction. The expected bands for type A were vague using ISO multiplex PCR method 1, whereas bright expected bands could be obtained in the identification of C.botulinum by the other two multiplex PCR method . Real-time multiplex PCR method could detect different types of C.botulinum simultaneously; however, classification should be carried out separately because fluorescent labels were the same. Conclusion Multiplex PCR method from FDA and multiplex PCR method 2 from ISO were relatively simple and could be recommended for C.botulinum surveillance in Sichuan Province.