Tephritidae is a large family that includes several fruit and vegetable pests. These organisms usually harbor a variegated bacterial community in their digestive systems. Symbiotic associations of bacteria and fruit flies have been well-studied in the genera Anastrepha, Bactrocera, Ceratitis, and Rhagoletis. Molecular and culture-based techniques indicate that many genera of the Enterobacteriaceae family, especially the genera of Klebsiella, Enterobacter, Pectobacterium, Citrobacter, Erwinia, and Providencia constitute the most prevalent populations in the gut of fruit flies. The function of symbiotic bacteria provides a promising strategy for the biological control of insect pests. Gut bacteria can be used for controlling fruit fly through many ways, including attracting as odors, enhancing the success of sterile insect technique, declining the pesticide resistance, mass rearing of parasitoids and so on. New technology and recent research improved our knowledge of the gut bacteria diversity and function, which increased their potential for pest management. In this review, we discussed the diversity of bacteria in the economically important fruit fly and the use of these bacteria for controlling fruit fly populations. All the information is important for strengthening the future research of new strategies developed for insect pest control by the understanding of symbiotic relationships and multitrophic interactions between host plant and insects.