More than 10% of insect species are known to harbor endosymbionts. These microbial symbionts have significant impacts on the development and other physiological processes of the insect hosts. We have analyzed the bacterial communities associated with the Hessian fly, Mayetiola destructor (Say), a major pest of Wheat, by using culture independent methods. Bacterial 16S rRNA genes were sequenced after PCR-amplification from DNA samples extracted directly from the whole larvae. Proteobacteria (~85%) was the dominant phylum in the 16S rRNA gene sequences obtained from M. destructor larvae, followed by Actinobacteria (~7%), Firmicutes (~3%) and Bacteroidetes (~3%). Out of a total of 72 proteobacterial sequences, bacteria belonging to γ-subdivision (~76%) were found to be the most abundant, followed by the α-subdivision (19%). Pseudomonas and Acinetobacter spp. were the most frequently isolated genera, while Achromobacter, Stenotrophomonas and Enterobacter spp. were less abundant. This study is the first survey on the symbiotic bacteria associated with the Hessian fly and will provide a foundation for future studies to elucidate the role of symbiotic bacteria on Hessian fly development and virulence. A better understanding of Hessian fly-microbe interactions may lead to new strategies to manage this pest.