In the past few years, the whole genome sequencing (WGS) analysis has shown its great value and potentials in the field of microbial heredity and variation characteristics, evolution and source tracking. This paper reviews the basic principles of WGS and introduces two main methods to interpret and analyze the WGS sequencing data by wgSNP and wgMLST. Then, the main characteristics of WGS such as discriminatory ability and sensitivity were compared with the other common molecular typing methods of PFGE and MLST. Also, it's illustrated that the current state-of-art of the WGS applied to the foodborne disease surveillance, identification of outbreaks and source tracking. Finally, the advantages of the WGS and the prospective of its future application in the foodborne disease surveillance and identification of outbreaks were briefly expounded.