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Recently, some research reports showed varied endophytic bacteria in the root nodules of some legumes, which attracts great interest in research field of rhizobia. Here, we reviewed the discovery, identification of some endophytic bacteria (Agrobacterium, non-symbiotic rhizobia, and other bacteria) in root nodules and their influence on symbiosis or plant growth, to understand the microecosystem of root nodule and to extend the field of rhizobia research.