The level and pattern of genetic diversity of seven natural populations of Chimonanthus nitens, an endangered plant bearing high ornamental and medicinal values, were investigated using inter-simple sequence repeat markers. 12 primers yielded 134 polymorphic bands. The genetic diversity was high at the species level (percentage of polymorphic loci, PPL=94.37%; Nei's gene diversity, h=0.2776; Shannon information index, I=0.4207), and relatively low at the population level (PPL=48.59%, h=0.1571, I=0.2373). Analysis of molecular variance (AMOVA) showed that the genetic variation among populations was 50.35%. Gene flow was restricted to a certain extent (0.6537). Seven populations were divided into three groups according to their geographical distribution and based on an unweighted pair-group method average dendrogram. A significant correlation (r=0.7744, P<0.01) was observed between the geographic distance and the genetic distance. Based on the results obtained from the current study, efficient and feasible conservation strategies for C. nitens were proposed.