Four species of synanthropic flies were trapped in downtown Kuala Lumpur: Chrysomya megacephala, Chrysomya rufifacies, Musca domestica, and Musca sorbens. Burkholderia pseudomallei, the organism causing melioidosis, was the dominant bacteria isolated from Chrysomya megacephala. Klebsiella oxytoca, commonly associated with nosocomial infections, was commonly isolated from Chrysomya megacephala, Musca domestica, and Musca sorbens. Aeromonas hydrophila, the bacteria causing gastroenteritis, was predominantly isolated from Chrysomya megacephala and also from Musca domestica and Musca sorbens. A total of 18 bacterial species was isolated from the synanthropic flies trapped. Burkholderia pseudomallei had been reported for the first time.