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The species Citrus hongheensis is an endangered species and the most primitive Citrus species with the most developed winged leaves. It is endemic to south Yunnan Province, southwest China, and only distributed in a very narrow area along the south bank of the Honghe river (the Yuanjiang river). By combining ISSR and morphological data from 11 populations, it shows that the species has rich genetic diversity among and within populations although the population is declining gradually. According to field and market surveys, the local Hani people have traditionally used C. hongheensis for a long time, such as the dried young fruits of the species as Chinese traditional medicine, leaves as food spice, as well as other organs. By collecting all existing knowledge of traditional and present uses, as well as further potential uses, we demonstrate that the species has good development prospects. Based on rich diversity, ethnobotanical uses, and a positive cultural environment, it was decided to choose four populations (YJNNDM, LCDX, HHDYJ, and YJYJYJ) of C. hongheensis for in situ conservation and artificial sexual reproduction. This will allow to develop new uses of the species, while providing indications for the conservation of other endangered species. [ABSTRACT FROM AUTHOR]