Endomicrobia are endosymbiotic bacteria that represent a deep-branching lineage in the phylum Elusimicrobia. They colonize the cytoplasm of termite gut flagellates and are specific for their flagellate hosts. Co-speciation of Endomicrobia with flagellates of the genus Trichonympha indicates a vertical transfer of the symbionts and an obligate dependence of the partners. The genome sequence of ‘Endomicrobium trichonym-phae’ provides first insights into the ongoing reductive evolution of the endosymbionts and their potential roles in the nitrogen metabolism of the partnership. The coexistence of endosymbionts and free-living relatives in termite guts make Endomicrobia a particularly good example for studying the evolution of an intracellular symbiosis in real time.