Miscanthus species have received considerable attention as a potential biomass source for renewable energy production because of their ability to produce high yields of biomass and adapt to a wide range of climates and soils. To explore the genetic diversity and phylogenetic relationship of Miscanthus species in China, we used 24 simple sequence repeat markers to genotype 100 natural populations representing all four Chinese Miscanthusspecies (M. sinensis Andersson, M. floridulus (Lab.) Warb. ex K. Schum. & Lauterb., M. sacchariflorus (Maxim.) Hack., and M. lutarioriparius L. Liu ex Renvoize & S. L. Chen). Based on phylogenetic, principal coordinate, and Structure analyses, we found that the 100 populations formed two major groups corresponding to sect. Triarrhena and sect. Miscanthus. Group 1 (i.e., sect. Triarrhena) was further subdivided into two subgroups corresponding to M. sacchariflorus and M. lutarioriparius; Group 2 (i.e., sect. Miscanthus) was subdivided into three subgroups, group 2a (M. sinensis populations in southern China), group 2b (M. sinensis populations in northern China), and group 2c (all the M. floridulus populations). Population genetics analyses indicated high levels of the genetic diversity at both population (H_E = 0.468–0.599) and species (H_E = 0.559–0.708) levels, indicative of the potential of these wild resources in future breeding programs. The species distribution modeling showed that M. sacchariflorus and M. lutarioriparius have experienced population reductions during the last glacial maximum and population expansion afterward; in contrast, M. sinensis and M. floridulus both underwent gradual population expansions from the last interglaciation to the present. We also suggest that M. floridulus originated from M. sinensis in southeast China through ecological speciation. The understanding of the evolutionary history and population dynamics of these species not only provides valuable information for further genetic improvement and breeding of this energy crop but also gives important insights into the origin and speciation processes of the Miscanthus species.