The development of next generation sequencing methods reduced the costs and improved the accuracy of sequencing. These advances accelerated its application in microbial genotyping and made it feasible to implement in foodborne pathogen subtyping and surveillance. Sequencing of all or nearly all nucleotides in a microbial genome provides superior discriminatory power that surpasses performance of other genotyping methods, such as pulsed field gel electrophoresis (PFGE) or multi-locus sequence typing (MLST), that have been used in pathogen subtyping prior to whole genome sequencing (WGS). This allows for a detailed comparison of similarity among strains of foodborne pathogens. WGS data provide a resource that can be used for assessment of strains' relatedness based on inferred phylogenetic relationships, evolution, and functional capacity, and has therefore become an invaluable tool in foodborne pathogen surveillance, characterization, and source tracking. In this chapter, we review sequencing technologies used for whole genome sequencing, implementation of WGS in foodborne pathogen surveillance by regulatory and public health agencies, WGS data analyses approaches, in silico prediction of relevant phenotypes, as well as challenges and opportunities related to international standardization of data analyses and communication.