The gut of lower termites harbor a complex microbial community, including eukaryotic flagellates and prokaryotic bacteria and archaea, which play important roles in the wood-cellulose digestion of these termites. The hindguts of lower termites are characterized with an enlarged paunch with steep oxygen and hydrogen gradient and not randomly distributed abundant microorganisms. The symbiotic flagellates in the gut of lower termites, which are normally associated with epibionts or endobionts, are phylogenetically affiliated with Trichomonadida, Hypermastigida and Oxymonadida. They endocytose wood particles and ferment the polysaccharide components to acetate, CO2 and H2, which are further metabolized by symbiotic prokaryotes as energy and nutrition sources in the termites. Cellulose genes such as glycosyl hydrolase family 45 have been identified in gut protists with molecular approach. Phylogenetic analysis have revealed that in the gut of lower termites, such as several Reticulitermites species, most of the dominant bacteria belong to phyla like "Termite group 1", Spirochaetes, Firmicutes, Bacteroidetes, and Proteobacteria. These bacteria clones normally form distinct termite clusters in phylogenetic trees, which show the existence of specific microbial diversity in the termite guts. Most of the symbiotic archaea in the gut of lower termites are methanogens and affiliated with the genus Methanobrevibacter by phylogenetic analysis and pure culture. The symbiotic bacteria and archaea may involve in the reduction of CO2 and the metabolism of N2 in these termite guts. However, the functions and metabolic mechanisms of the symbiotic flagellates and prokaryotes in the gut of lower termites are still remaining to be further elucidated.