The genetic diversity of seven natural populations of Rhododendron kiangsiense Fang in Jiangxi Province was systematically analyzed by using inter-simple sequence repeat (ISSR) molecular marker technology, and targeted conservation and management strategies were proposed based on the research results. The results show that the three selected primers (UBC825, UBC826, and UBC827) amplify a total of 44 polymorphic loci from the DNAs of 49 individuals across the seven populations, with the percentage of polymorphic loci reaching 86.3%. Among the test populations, the population of Mingyue Mountain, Yuanzhou District, Yichun City, exhibits the highest percentage of polymorphic loci (56.9%), followed by the population of Nanfengmian, Suichuan County, Ji'an City (33.3%), while the percentages of polymorphic loci of remaining populations all below 30%. The numbers of observed alleles and effective alleles, Nei's gene diversity index, and Shannon's information index of the test populations are 1.862 7, 1.357 7, 0.228 0, and 0.360 0, respectively, the total genetic diversity index is 0.205 3, the genetic diversity index within populations is 0.082 1, the genetic differentiation coefficient is 0.600 0, and the gene flow is 0.333 3. The genetic similarity coefficient is the largest (0.946 4) and the genetic distance is the smallest (0.055 0) between the population of Shuikou, Jinggangshan City, Ji'an City and the population of Nanfengmian, Suichuan County, Ji'an City, whereas the genetic similarity coefficient is the smallest (0.745 1) and the genetic distance is the largest (0.294 3) between the population of Wugong Mountain, Luxi County, Pingxiang City and the population of Longtan, Jinggangshan City, Ji'an City. The clustering analysis results among individuals and populations reveal that the genetic relationships between the population of Nanfengmian, Suichuan County, Ji'an City and the populations of Shuikou, Longtan and Bamian Mountain, Jinggangshan City, Ji'an City are close, and those between these four populations and the population of Yangshimu, Anfu County, Ji'an City, the population of Wugong Mountain, Luxi County, Pingxiang City, and the population of Mingyue Mountain, Yuanzhou District, Yichun City are distant. In conclusion, the seven natural populations of R. kiangsiense in Jiangxi Province exhibit low genetic diversity, substantial genetic differentiation and weak gene flow among populations, and low genetic variation within populations. In view of the current survival status and genetic diversity characteristics of the natural populations of R. kiangsiense, it is recommended to implement conservation and management strategies, such as in situ conservation, artificial pollination and gene flow management, ex situ conservation and reintroduction, enhancing monitoring and research.