It is estimated that the Formosan subterranean termite, Coptotermes formosanus Shiraki, causes over a billion dollars per year in economic damage in the United States. This invasive and aggressive pest species is dependent on its gut flora for survival (three species of protists and an undetermined number of bacteria). The lack of information about the bacterial gut flora of C. formosanus is due to limited success of culturing bacteria in natural communities. The main scope of this study was to investigate the bacterial diversity in the gut of C. formosanus, i.e., the number and proportions of different bacterial taxa. We collected workers from three colonies in Louisiana, and have extracted, cloned and sequenced the communal bacterial DNA. Bacteria were classified according to the closest match of their 16S sequence in GenBank. To date, we have sequenced 165 bacterial strains from the three termite colonies. We found 19 different ribotypes of bacteria from eight different taxonomic groups the majority of which were novel species. Bacteroides and Treponema represented the most abundant (66%) and diverse groups (seven groups / 9%), respectively. Amongst the remaining groups are representatives of the new phylum known as “Endomicrobia”(1%), a symbiont of the protists that live within the gut of C. formosanus and a member of the Mycoplasmataceae (1%), a bacteria which lacks a cell wall and behaves like a parasite. An understanding of the diversity of the bacteria in the termite gut will be helpful in identifying tools and targets for termite control.