The so-called mutualistic symbiotic microbes (MSM) can colonize other organisms to build a mutual symbiotic system. MSM mainly include mutualistic symbiotic bacteria, mutualistic symbiotic actinomycetes and mutualistic symbiotic fungi. MSM are diverse, with a wide distribution and rich in species diversity, involving those in procaryotae and kingdom fungi. MSM colonize human body, animals, plants, algae, or other fungi, and can build their respective reciprocal symbiotic systems, and then form a wider symbiotic network to play irreplaceable physiological and ecological functions. On the basis of introducing the concept of MSM, this paper summarizes the progress of MSM diversity research, problems existing in the current research, and the work in the future. The results of MSM diversity research are expected to provide basis for the development of MSM application.