The Formosan subterranean termite, Coptotermes formosanus Shiraki, is an invasive pest species that causes billions of dollars in economical damage in the U.S. The survival of this termite is dependent on its gut flora (three species of protozoa 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. Molecular techniques (PCR amplification of 16S rRNA genes) provide the opportunity to study the bacterial inhabitants of the termite gut in a culture-independent approach. In this study we investigated the bacterial diversity in the gut of C. formosanus, i.e., the number and proportion of different bacteria taxa. We collected termites from three colonies from various regions in Louisiana, and have extracted, cloned and sequenced the communal bacterial DNA. Bacteria were classified according to the closest match of their 16S sequences in GenBank. To date, we have sequenced 65 bacterial strains from one termite colony. We found 11 different strains of bacteria from three different groups (Bacteroides, Spirochaeta, and Treponema) inclusive of a strain that is currently described as an “unidentified bacterium” but most closely resembles Bacteroides (determined by sequence analysis). Bacteroides was the dominant group among the gut flora (over 70%). The bacteria taxa identified in the gut of C. formosanus in this study using culture independent 16S sequencing were different from the bacteria previously cultured from the gut of the same termite species.