Approximately 76 million people suffer from foodborne illnesses in the U.S. annually at an average cost to the U.S. economy of $15 billion. Many pathogenic bacterial species have been implicated in foodborne diseases, with infections caused by Salmonella and Campylobacter species occurring at higher frequencies than those caused by other species. In this study we present MST as a means of determining the food animal of origin of Campylobacter and Salmonella. We have investigated serotyping, antimicrobial susceptibility, pulse-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) for their capacities to distinguish Campylobacter and Salmonella isolates from pigs, cattle, turkey and chickens. For Campylobacter, preliminary analysis of the data suggests that PFGE and MLST provide better discriminatory power than biochemical profiles or serotyping. For Salmonella, serotyping appears to be the best method for certain strains, namely S. Dublin and S. Choleraesuis isolates, in which over 99% are from cattle and swine, respectively. The results from this study could aid in determining the food animal species from which Salmonella or Campylobacter may have originated. Further, the methods can be used as an example for future MST studies of other foodborne pathogens. Data from these studies will aid the FDA’s ability in making science-based regulatory decisions about food safety.