Investigating the genetic diversity and population structure is important in conserving narrowly distributed plants. In this study, 90Clematis acerifolia(C.acerifolia) plants belonging to nine populations were collected from the Taihang Mountains in Beijing, Hebei, and Henan. Twenty-nine simple sequence repeats (SSR) markers developed based on RAD-seq data were used to analyze the genetic diversity and population structure ofC.acerifolia. The mean PIC value for all markers was 0.2910, indicating all SSR markers showed a moderate degree of polymorphism. The expected heterozygosity of the whole populations was 0.3483, indicating the genetic diversity of bothC.acerifoliavar.elobataandC.acerifoliawere low. The expected heterozygosity ofC.acerifoliavar.elobata(He = 0.2800) was higher than that ofC.acerifolia(He = 0.2614). Genetic structure analysis and principal coordinate analysis demonstrated thatC.acerifoliaandC.acerifoliavar.elobatashowed great genetic differences. Molecular variance analysis (AMOVA) demonstrated that within-population genetic variation (68.31%) was the main contributor to the variation of theC.acerifoliapopulations. Conclusively,C.acerifoliavar.elobatahad higher genetic diversity thanC.acerifolia, and there are significant genetic differences betweenC.acerifoliaandC.acerifoliavar.elobata, and small genetic variations within theC.acerifoliapopulations. Our results provide a scientific and rational basis for the conservation ofC.acerifoliaand provide a reference for the conservation of other cliff plants.