Protist-dependent termites rely on a mutually obligate symbiosis with populations of protists that colonize the hindgut to digest lignocellulose. Protists are transmitted vertically amongst termite colonies so that each member of a termite species shares protist symbionts with its nestmates. These protist populations are therefore thought to be specific to their host and may serve as an indicator of the evolution and diversification of both termites and protists. However, evolutionary signals may be misinterpreted or interrupted if protists are misidentified, lost, or transferred between termite species. The protist genus Trichonympha is one such taxon whose constituent species deviate from typical phylogenetic patterns of vertical inheritance. In this study, light microscopy, single cell isolation, and 18S sequencing were used to determine the morphology and phylogeny of Trichonympha from Reticulitermes spp., resulting in the discovery of 2 novel species and the revision of the longstanding species, Trichonympha agilis. These results suggest the importance of phylogeny over morphology in species determination, and the confirmation that multiple termite species host the same protist symbionts.