In the current study, samples of 50 synanthropic flies were collected from each of five rural locations used for domestic animal husbandry (specifically a cattle barn, a dog pound, a horse stable, and a pigpen). Flies were examined using a variety of microbiological methods to determine the pathogenic agents that they carried. The most frequently sampled species were Musca domestica (L.) (51%) followed by Stomoxys calcitrans (L.) (24%). All fly species were found to carry an array of different pathogenic bacterial and fungal species. Among these were human pathogens such as Campylobacter jejuni and Escherichia coli-strains (EHEC, EPEC, and ETEC) and the fungi Candida albicans and Candida tropicalis. The germs could be detected in the intestines as well as on the exoskeletons of the flies. The current study confirms and supplements the general knowledge about pathogens that may be transmitted to domestic animals and humans by synanthropic flies.