It is well understood that multiple factors contribute to the dynamics of the gut microbiota residing in an animal host. However, little is known about how bacterial microbiotas change during and after recent speciation events in their hosts. In this Evolution paper, Vanderbilt researchers report that incipient species share more similar bacterial species than divergent species, even when the animal species are reared on identical diets. Results demonstrate that a microbial succession occurs from larval development to adulthood, and that the evolution of microbial symbiont communities are closely allied with that of their host's divergence. Thus, microbiotas may be thought of as extended phylogenetic markers of the host’s genotype. The implications for studies of microbial symbiosis and speciation are discussed.