Coptotermes formosanus Shiraki and Coptotermes gestroi (Wasmann) (Blattoidea: Rhinotermitidae) are invasive subterranean termite pest species with a major global economic impact. However, the descriptions of the mutualistic protist communities harbored in their respective hindguts remain fragmentary. The C. formosanus hindgut has long been considered to harbor three protist species, Pseudotrichonympha grassii (Trichonymphida), Holomastigotoides hartmanni, and Cononympha (Spirotrichonympha) leidyi (Spirotrichonymphida), but molecular data have suggested that the diversity may be higher. Meanwhile, the C. gestroi community remains undescribed except for Pseudotrichonympha leei. To complete the characterization of these communities, hindguts of workers from both termite species were investigated using single-cell PCR, microscopy, cell counts, and 18S rRNA amplicon sequencing. The two hosts were found to harbor intriguingly parallel protist communities, each consisting of one Pseudotrichonympha species, two Holomastigotoides species, and two Cononympha species. All protist species were unique to their respective hosts, which last shared a common ancestor~18 MYA. The relative abundances of protist species in each hindgut differed remarkably between cell count data and 18S rRNA profiles, calling for caution in interpreting species abundances from amplicon data. This study will enable future research in C. formosanus and C. gestroi hybrids, which provide a unique opportunity to study protist community inheritance, compatibility, and potential contribution to hybrid vigor. COPTOTERMES formosanus Shiraki and Coptotermes gestroi (Wasmann) are subterranean termite species within the family Rhinotermitidae (Krishna et al. 2013). Coptotermes formosanus (Formosan subterranean termite) is a warm temperate/subtropical species native to southern China and Taiwan, while C. gestroi (Asian subterranean termite) is a tropical species native to Southeast Asia (Li et al. 2009). Their most recent common ancestor lived~18 million years ago and gave rise to multiple descendant lineages, from which C. formosanus and C. gestroi emerged in allopatry within the last~5-10 million years (Bourguignon et al. 2016). However, human activity has led to the spread of both species beyond their native ranges, and they are now established in sympatry in at least three distinct areas: Taiwan, Hawaii, and southeastern Florida (Chouvenc et al. 2016; Evans et al. 2013; Scheffrahn and Crowe 2011; Su et al. 2017). Coptotermes mature colonies can contain several million individuals and