Single Nucleotide Polymorphism (SNP) refers to the DNA sequence polymorphism caused by the variation of a single nucleotide at the genome level. With the development of high-throughput sequencing technology, whole genome sequencing has been included in newly issued regulations and guidelines in the fields of food, medicine, feed, etc. Whole genome sequence-based SNP analysis (WGS-SNP) provides as a high-resolution method for precise identification and typing of microorganisms. Compared with commonly used methods such as RAPD, MLST, and RFLP, WGS-SNP has the advantages of high resolution, stable data, and easy comparison of results of inter- laboratory study. It has a wide range of applications in the analysis of microbial strain level identification, traceability of contaminated bacteria, genetic stability of bacterial strains, etc.