The hindgut of feeding termites that feed on wood and litter contains a diverse population of bacteria and protists that contribute to the carbon, nitrogen, and energy requirements of the termite. For understanding the ecological balance in the termite gut, detailed knowledge about the composition of the microbial gut flora is imperative, i.e., the numbers and relative proportions of the microbial taxa and the variability in the microbial composition among different termite colonies and living conditions of termites should be described. Therefore, we isolated and enumerated eight bacterial morphotypes from the gut of the Formosan subterranean termite, Coptotermes formosanus Shiraki. Five morphotypes (three isolates of lactic acid bacteria, isolates of the family Enterobacteriaceae and isolates belonging to the genus Dysgonomonas) were found frequently in all termite colonies. Three additional morphotypes were found sporadically and were considered to be transient flora. We compared the proportions of the three lactic acid bacteria isolates and the Enterobacteriaceae among three different termite colonies. Furthermore, we investigated the shift in proportions of these four major morphotypes depending on whether bacteria were isolated from freshly collected termites or from termites reared in the laboratory under seminatural conditions (in arenas on wood) or artificial conditions (in petri dishes on filter paper). Differences in the culturable microbial composition were not significant among termite colonies, or between field-collected termites and termites reared under seminatural conditions in the laboratory. However, we found significant shifts in the microbial composition between field-collected termites and termites reared on filter paper.