In the current study samples of Musca domestica the common house flies were collected from Wadi Eldawaser at different urban and rural locations named Alkhamasin, Sulayel and Tathleth (January 2010 till January 2011). Flies were examined using kits and routine cultural methods for microbiological identifications to determine the pathogenic bacterial species that they carried externally and internally. A total of 360 house fly were collected to isolate bacteria, 227 (63.05%) of the examined flies were found to carry different pathogenic bacterial species. The most frequent pathogens were found to be the enteric human pathogens such as Escherichia coli (18.7%), Klebsiella pneumoniae (7.5%), Proteus vulgaris (6.3%).The other pathogens were Shigella dysentery (5.9%), Bacillus subtilis (5.3%), Staphylococcus aureus (5.1%), Psodomonas aeruginosa (3.5%) and Salmonella paratyphi (2.7%). The highly pathogenic bacteria which was isolated three times and detected by the polymerase chain reaction (PCR) , both Mycobacterium tuberculosis (causative agent of Tuberculosis ) and Chlamidiae trachomatis (causative agent of Trachoma). Most of the isolated bacterial species could be found in both cold and worm season. once time was isolated both Streptomyces sp. which is a chitinase producing bacteria from Elsulayel area as the first record reported and Bacillus thuringiensis which is known to be an effective bio-control agent against insects. The current study gives the attentions to the pathogenic bacterial species that may be transmitted to humans by this nuisance flies which is a serious health threats for induction of epidemiology. . Key words: Musca, synanthropic fly species, Empty Quarter, Public health, Vectors of disease, bacteria.