Prokaryotic associations with gut protists of the termite Coptotermes formosanus were investigated based on 16S rRNA gene sequences. An endosymbiotic methanogen of Spirotrichonympha leidyi phylogenetically grouped with endosymbionts of other gut protists in the genus Methanobrevibacter, seemed to be unrelated to the host protist phylogeny. Three different lineages of ectosymbiotic spirochetes in the genus Treponema were identified in single cells of Holomastigotoides mirabile, indicating their simultaneous occurrence. Although these symbionts represented mere minor populations in the gut, their phylogenetic assignments suggest a common symbiotic relationship involving H2 metabolism.