Salmonella remains one of the leading causes of food-borne illness in the United States, and many key questions regarding the introduction and persistence in animal production systems still remain. In order to understand the ecology of Salmonella within an integrated commercial broiler production system, 289 Salmonella enterica were recovered from two integrated poultry farms during the production and processing of seven consecutive flocks. The variety and prevalence of Salmonella serotypes differed between farms. Overall, 15 serotypes were identified, with the most common being Typhimurium (55%), Montevideo (7.9%), Kentucky (9%), and Enteritidis (9.7%). Salmonella Typhimurium and Enteritidis isolates recovered from processed carcasses from Farm One were further characterized using pulsed-field gel electrophoresis (PFGE), and were shown to be indistinguishable from isolates recovered from the poultry house environment and mice trapped on this farm. Additionally, the same broiler S. Typhimurium and S. Enteritidis strains, identified by PFGE, were also isolated from samples taken at a company breeder farm, suggesting vertical transmission of these Salmonella serotypes in this poultry production system. Results indicate that management practices at the breeder level may have a profound effect on the transmission and persistence of salmonellae within an integrated production system, as well as on the potential contamination of poultry-derived products.