This study aims to evaluate flies as a vector for foodborne pathogens. For this purpose, several flies were collected from different sites from rural areas. These flies were then analyzed for the presence of Enterobacteriaceae, Escherichia coli, Staphylococcus coagulase positive, and Listeria monocytogenes. Another aim of this study was to evaluate some virulence factors of the collected pathogens: susceptibility to some antibiotics and the presence of enterotoxigenic S. aureus. The results showed that flies in the presence of animals demonstrated a significantly higher prevalence of the studied pathogens than those collected in the kitchens, and kitchens situated in the closest proximity to the animal husbandry had a higher count than the kitchens in private houses. Enterobacteriaceae was the indicator organism with the highest microbial counts followed by E. coli and S. aureus. Listeria monocytogenes was not detected from any of the collected flies. The antimicrobial susceptibility test showed that the bacteria carried by the flies possessed multiantibiotic resistance profiles, and enterotoxin A was produced by 17.9% of the confirmed S. aureus isolates. These results demonstrate that flies can transmit foodborne pathogens and their associated toxin and resistance and the areas of higher risk are those in closer proximity to animal production sites.