Phenotype-based and DNA-based subtyping methods allow for differentiation of bacterial isolates beyond the species and subspecies level. Bacterial subtyping methods not only have improved our ability to detect and track foodbome disease outbreaks, but also represent tools to track sources of bacterial contamination throughout the food system. The use of subtyping methods furthermore provides an opportunity to better understand the population genetics, epidemiology, and ecology of different foodbome pathogens. The last 5 years have seen tremendous advancement in the development of sensitive, rapid, automated, and increasingly easy-to-use molecular subtyping methods for a variety of different bacterial foodborne pathogens. This review will highlight key aspects of different subtyping methods for bacterial foodborne pathogens and provide examples of their applications in public health, food safety, epidemiology, and population genetics. Molecular subtyping and characterization methods may also facilitate the development of a novel framework for tracking, preventing, and regulating foodborne bacterial diseases, which is based on evolutionary relationships and genetic characteristics rather than traditional species definitions.