The microbial community in the gut of termites, comprising both cellulolytic flagellated protists and diverse prokaryotes, is responsible for the efficient degradation of recalcitrant lignocellulose. The complex nature of the community and the formidable unculturability of most members have hampered detailed microbial studies. Comprehensive phylogenetic descriptions of the community members based on their rRNA gene sequences still provided little information about their functions because the community contained enormous novel microbial diversity. A prominent feature of the community is the presence of a variety of bacterial associations with the cells of gut flagellates in the cytoplasm (endosymbioses) and/or on the cell surface (ectosymbioses), and the bacterial symbionts were identified phylogenetically and in situ. The associated bacteria were usually specific for host flagellates and they likely have cospeciated at least within flagellate genera. The associated bacteria corresponded to the most abundant members of the community, and thus the voluminous cellulolytic flagellates and their associated bacteria should play central roles in the gut metabolism. Studies on their functions and mutual interactions have started through complete genome analyses of the associated bacteria and meta-EST (Expressed Sequence Tags) of the host flagellates. These advances have gradually unveiled how this symbiotic complex functions to efficiently utilize lignocellulose.