Protist-dependent termites (non-Termitidae) and the wood roach Cryptocercus accomplish a feat which is crucial to ecological processes and detrimental to man-made structures: the digestion of wood and other cellulose-rich materials. However, the symbiotic protists harboring in termite hindguts aid in the digestion of the wood particles after it has been ingested by the insects. Termite hindgut symbionts have been passed from generation to generation through proctodeal trophallaxis for about 150 million years. Because of this close relationship, they have co-diversified with their hosts, splitting into new lineages through time. While hindgut communities within some termite species have been analyzed and this number is increasing over time, a study of the protist communities across lower termites is lacking. Using long-read sequencing of the rRNA operon, a supported phylogeny has been made to infer a preliminary number of protist species belonging to the order Cristamonadida within termite hindguts, the relationships of these protist species, and determine the extent of cospeciation between termites and their hindgut endosymbionts.