Due to the specific physiological nature of the termite gut, scientists have had difficulty culturing and thereby studying the resident microorganisms. The advent, however, of methods for analyzing nucleotide data made the development of culture-independent methods possible. The authors present the results of on-going research exploring the diversity of symbiotic prokaryotes within the gut of termites. 16S rRNA sequence data is utilized to explore the phylogenetic relationships of the bacterial symbionts inhabiting the midgut and hindgut regions of Reticulitermes sp. These data provide a basic framework for researchers interested in targeting the gut flora as an indirect control method against termites.