The fruit fly Anastrepha obliqua harbors three kingdoms of life in its intestinal tract.

The fruit fly Anastrepha obliqua is an economically important pest for mango fruits in Mexico. The sterile insect technique is used to control this pest; it involves mass production and release of sterile flies to reduce reproduction of the wild population. As noted in different tephritidae, the performance of sterile males may be affected by the assimilation of nutrients under mass-rearing conditions. In the wild, the flys life cycle suggests the acquisition of different organisms that could modulate fitness and physiology of the fly. Therefore, the microorganisms lodged in the gut may be determinative. For A. obliqua, there is no information regarding microorganisms other than bacteria. This study analyzed bacteria, fungi, and archaea communities in the A. obliqua gut through denaturing gradient gel electrophoresis (DGGE) profile of 16S and 18S ribosomal DNA markers. Besides, 16S sequencing and phylogenetic analysis provided a better description of bacteria, and archaea communities. We found that wild flies presented higher microbial diversity than laboratory samples. Phylogeny analyses of wild samples suggest the presence of microbial species related to fructose assimilation while laboratory microbial species suggest the presence of microorganisms leading to a specialized metabolism to process yeast as result of the consumption of an artificial diet. Here, the archaea kingdom is suggested as an important player in fly metabolism. This is the first report of the intestinal microbial (bacteria, archaea and fungi) composition of A. obliqua, which will aid in our understanding of the role of microorganisms in the development and physiology of the flies.