Many animals have symbiotic relationships with gut microbes that influence their hosts’ physiology and behavior. One of the most characterized symbiotic systems is that of termites and their intestinal microorganisms, which is essential for wood digestion. In termite colonies, workers engage in foraging, while king and queen specialize in reproduction. The microbiota in king and queen may play an important role in colony fitness, however, few studies focused on their interactions. Here we evaluated the intestinal microbial community in the kings and queens of termites throughout their life cycles and among species. Our results suggested that, in the incipient colony, a young king and queen of a Japanese termite, Reticulitermes speratus increased their intestinal protists and digested them to obtain nutrition for investment to offspring. In a mature colony, the king and queen of R. speratus completely lost intestinal protists and possessed a specific bacterial community. By interspecies comparison, we showed that king and queen of primitive species had intestinal protists, while king and queen of derived species did not. Considering that queens in derived species lay more eggs than those of primitive species, our results imply the existence of a trade-off between reproduction and possessing intestinal protists in reproductives.