The domestic pig is an important source of human salmonellosis, and houseflies are potential mechanical vectors of foodborne Salmonella pathogens. In 2005, we recovered 144 Salmonella isolates from flies and swine stool samples from 11 farms in Taoyuan County and Hsin Chu County (northwestern Taiwan). A total of 71.5% of the isolates were resistant to at least three antibiotics. There were a total of 14 serotypes, and 8 of these serotypes were present in both flies and swine stool samples. Some multidrug-resistant Salmonella strains coming from different swine farms were found to have identical pulsed-field gel electrophoresis (PFGE). Among four common serotypes, we identified 18 PFGE patterns, 8 of which were present in flies and swine stools. The similarity in PFGE profiles between isolates from swine and flies in different farms indicate the potential of flies to serve as a vector for transmission.