Termite hindgut symbionts serve an important role in meeting the nutritional requirements of termites. Studies quantifying Reticulitermes protist communities have been conducted using a variety of methods, thus making comparisons between studies difficult. Protist species are involved in separate stages of metabolism and, because termite life stages are fed different diets, their protist communities should reflect that. We compared methods used to estimate termite hindgut protist populations and propose a single technique for ease and accuracy. We looked at protist communities from four life stages of Reticulitermes flavipes (Kollar), Reticulitermes virginicus (Banks), and Reticulitermes hageni Banks, and found workers and nymphs have the largest population of protists, followed by soldiers, with the smallest populations in alates. In addition we showed these communities can be used to identify termites using the most common life stage, workers. We showed protist communities are not a good indication of termite colony health.