Yunnan, located in southwestern China, harbors more than 19,000 higher plants, which represents the highest plant diversity in the country. However, plant diversity in Yunnan faces enormous threats today, including habitat destruction and fragmentation, environmental pollution, and over-exploitation of natural resources. Despite recent efforts to protect biodiversity, there are still thousands of threatened species, some of which have become extinct. We analyzed available data to gain a greater understanding of plant diversity and the status of plant conservation in Yunnan. We found that southern, southeastern, and northwestern Yunnan are hotspots of total species, endemic species, specimens, new species and threatened species, whereas southeastern Yunnan is a hotspot for plant species with extremely small populations. Moreover, we found that there are still conservation gaps and poorly protected areas in central, eastern, and northeastern Yunnan. We conclude that conservation of plant diversity in Yunnan requires modern field investigation, systematic research, the development of comprehensive databases, and government support. We recommend that conservationists pay more attention to building and improving functional protection systems and popularizing science.