<jats:title>Abstract</jats:title><jats:p><jats:italic>Coptotermes formosanus</jats:italic> Shiraki and <jats:italic>Coptotermes gestroi</jats:italic> (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 <jats:italic>C. formosanus</jats:italic> hindgut has long been considered to harbor three protist species, <jats:italic>Pseudotrichonympha grassii</jats:italic> (Trichonymphida), <jats:italic>Holomastigotoides hartmanni</jats:italic>, and <jats:italic>Cononympha</jats:italic> (<jats:italic>Spirotrichonympha</jats:italic>) <jats:italic>leidyi</jats:italic> (Spirotrichonymphida), but molecular data have suggested that the diversity may be higher. Meanwhile, the <jats:italic>C. gestroi</jats:italic> community remains undescribed except for <jats:italic>Pseudotrichonympha leei</jats:italic>. 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 <jats:italic>Pseudotrichonympha</jats:italic> species, two <jats:italic>Holomastigotoides</jats:italic> species, and two <jats:italic>Cononympha</jats:italic> 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 <jats:italic>C. formosanus</jats:italic> and <jats:italic>C. gestroi</jats:italic> hybrids, which provide a unique opportunity to study protist community inheritance, compatibility, and potential contribution to hybrid vigor.</jats:p>