The Mediterranean fly (Medfly), Ceratitis capitata causes important economic and agricultural losses due to its peculiar ability to invade and adapt to different climates throughout tropical and subtropical regions. Traditional control methods should be implemente by innovative tools among which those based on nsect symbiont seem very promising. Our study aimed to characterize the microbial communities of different anatomical districts (gut and reproductive organs) of three different strains of C. capitata, to determine whether selected symbionts could be translated into potential tools for the symbiotic control of medfly. While confirming the presence of Asaia in both organs, we revealed for the first time the presence of Propionibacterium and Chroococcidiopsis in the reproductive organs of Medfly. These findings paves the way for the development of control methods based on the use of symbiotic bacteria.