Insects form an extremely large group of animals and bear a consequently large variety of associated microbes. This microbiota includes very specific and obligate symbionts that provide essential functions to the host, and facultative partners that are not necessarily required for survival. The Tephritidae is a large family that includes many fruit pests such as the Mediterranean fruit fly (the medfly, Ceratitis capitata) and the Olive fly (Bactrocera oleae). Community and functional analyses showed that the microbiota of both flies contribute to their diet, and affect host fitness parameters. The analysis of the microbiota's community structure of mass-reared, sterilized medfly males used in the sterile insect technique revealed a strong reduction in Klebsiella spp. compared with non-sterile and wild flies. Inoculation of sterile males with this gut population affected female mating behaviour as they preferentially mated with inoculated versus non-inoculated males. These studies suggest that control can be significantly improved by manipulating symbionts in pest animals.