Technical Abstract: The incidence of food-borne illnesses from pathogenic bacteria (e.g. Escherichia coli and Salmonella spp) remains relatively constant despite the use of various abatement practices for reducing them. Methods to rapidly detect and discriminate between closely related pathogens are required to identify sources of food-borne illnesses. Pulsed field gel electrophoresis (PFGE) is currently considered the 'gold standard' molecular method for sub typing pathogens by the Centers for Disease Control and Prevention (CDC). The PFGE method requires four days to complete, thus slowing identification of a disease source. Application of amplicon length polymorphism (ALP) represents a novel genome-based molecular method to detect, identify, and confirm the source of an outbreak. ALP can discriminate amongst related strains of pathogens to the same or to a higher degree of resolution than PFGE, while also reducing both the time and expense required to confirm the source responsible for the food-borne illness. The theory underlying ALP and its ability to differentiate amongst closely related pathogens, such as Escherichia coli and Salmonella spp. will be described. In principle, ALP can be applied to differentiate any group of closely related strains of bacteria. Since nearly 1100 microbial and archaeal genomes have been completely sequenced, with several hundred other sequencing projects underway, the ALP method should have widespread applicability.