The role of Musca domestica in the transmission of infectious diseases cannot be overemphasized. This study was therefore aimed at determining the natural carriage of Salmonella and Shigella species on the body parts of Musca domestica (housefly) using standard procedures. A total of 100 houseflies were collected randomly across different locations in Ago iwoye by using Mangifera indica (mango) as bait for catching them in tight fitted pre-sterilized bottles. The collected houseflies were transported to the Microbiology Laboratory of the Olabisi Onabanjo University for processing not later than 4hours after collection. Results obtained depict the natural carriage of Salmonella typhi and Shigella dysenteriae in all the sampled locations except at Bobo dumpsite where no Salmonella typhi was recovered and also at Adesegun where both Salmonella typhi and Shigella dysenteriae were not found. Both Salmonella typhi and Shigella dysenteriae accounted for 80 (47.1%) and 90 (52.9%) respectively to give a total of 170 (100%) bacterial isolates. The zones of inhibition of the isolated organisms when interpreted using the NCCLS interpretative chart revealed that approximately 87.8% and 93.8% of the Shigella dysenteriae and Salmonella typhi isolated from the houseflies were resistant to the different antibiotics tested respectively. It can thus be concluded that Musca domestica are natural carriers of multi-drug resistant Salmonella and Shigella which should be viewed as a potential vector for the transmission of both shigellosis and salmonellosis in the studied area