Firmiana major (Malvaceae) is a dominant tree species in hot, arid valleys with savanna vegetation in southwest China. Due to severe human disturbance, the populations of F. major declined sharply and was once considered extinct in the wild. Until 2020, eight populations of F. major were found by our investigation and it was listed as a Plant Species of Extremely Small Populations (PSESP) in Yunnan Province, China, for urgent rescuing during the next decade. To guide its conservation, the genetic structure, demographic history, and distribution model were studied. Four genetic groups of F. major were revealed and their divergence times coincided with warming periods during the last glacial stage. The distribution model showed a narrow habitat for F. major around the hot, arid areas of Yuanmou Basin, Jingsha arid-hot valleys and their adjacent areas, which enhanced its endangered situation. Based on the study, several conservation suggestions for F. major were proposed including adopting its germplasms with better drought tolerance for afforestation in this area. • Firmiana major is an endangered yet dominant tree that has potential to be a native greening species in savanna vegetation. • We found four genetic groups of F. major and one group showed climatic differentiation from other groups. • Divergence time of F. major was related to the warm periods in the last glacial stage. • The study predicted a relatively narrow distribution of F. major in hot, arid areas which enhanced its endangered situation. • We provided population recovery goals and conservation strategies for F. major based on the results.