Previous studies indicate subterranean termite protist communities are qualitatively similar within termite species but differ in relative species abundance between castes. We investigated protist communities from four castes of Reticulitermes flavipes (Kollar), Reticulitermes virginicus (Banks), and Reticulitermes hageni Banks. We used a standardized counting technique and found termite workers and early stage nymphs had the largest population of protists, followed by soldiers and alates. R. flavipes workers averaged 59,000 flagellates compared with 21,000 in R. hageni and 14,000 in R. virginicus. We recorded two new genera, Microjoenia Grassi and Monocercomonas Grassi, from R. virginicus. We identified eight protist species from R. hageni, whereas only four have been previously noted. This is the first report of Dinenympha fimbriata Kirby, Holomastigotes elongatum Grassi, Monocercomonas Grassi, Pyrsonympha minor Powell, Spirotrichonympha flagellata (Grassi), and Trichonympha agilis Leidy from R. hageni. Across all termite species, we found that workers, nymphs, and soldiers had similar relative protist species abundances, with alates being different. The results also demonstrated the utility of using the relative abundance of indicator protist species to identify these three subterranean termite species. The presence of Dinenympha gracilis can be used to distinguish R. flavipes from R. virginicus and R. hageni. R. virginicus has a greater abundance of T. agilis, compared with the other two termite species. The relative abundance of D. fimbriata and Pyrsonympha from R. hageni is greater than those found in both R. flavipes and R. virginicus.