This dataset contains data from the list of the National Key Protected Wild Plants (the first and second batches) officially approved by the State Council, 1898 plants were recorded in the information system of the Chinese Rare and Endangered Plants. The dataset includes: name of species (Latin Name), Place (counties in China), Latitude and Longitude (coordinates of the Place), MAP (Mean annual precipitation), MAT (Mean annual temperature) and MAH (Mean annual humidity), Altitude (Vertical distribution of habit of the rare and endangered plants), Habit (Habit type of the rare and endangered plants), Species density (number of plant species/ log (area of a county)).

In the study, we collected information on climate, altitude, habitat, and distribution of rare and endangered plants in China, to determine their habitat characteristics, geographical distribution, and the relationships between environmental factors and species density. We found that rare and endangered plants tend to distribute in warm, humid, and forested habitats. Mountains, rather than plains, hills, wind-accumulated landforms, tablelands, lakes, and glaciers, can provide mesophytic and less-disturbed refuges for rare and endangered plants. In particular, medium and medium high-altitude mountains located in monsoon-dominated regions with high precipitation, temperature, and humidity provide diversified habitats for species of rare and endangered plants with high density.

According to the list of the National Key Protected Wild Plants (the first and second batches) officially approved by the State Council, 1898 plants were recorded in the information system of the Chinese Rare and Endangered Plants (ISCREP, http://www.iplant.cn/rep/). The geographical distributions of these plants in different counties, altitude ranges, and habitats were collected from the database of the Flora of China (http://www.iplant.cn/foc/).

Meteorological datasets from 1981 to 2010 were obtained from the National Meteorological Information Center (http://data.cma.cn/) that monitors 2086 national meteorological stations in China (Fig. S1). The annual average of each climatic factor was obtained by averaging the monthly data from each observation station. The altitudes of the 2086 national meteorological stations were collected from meteorological datasets to determine the distribution of altitude in China.

The readme file contains an explanation of each of the variables in the dataset, its units. Information on how the measurements were done can be found in the associated manuscript referenced above.