Sauvagesia rhodoleuca (Ochnaceae) is an endangered plant that is endemic to southern China. The levels of genetic variation and patterns of population structure in S. rhodoleuca were investigated using inter-simple sequence repeat markers. Eleven primers were used to amplify DNA samples from 117 individuals, and a total of 92 loci were detected. Our results indicated that genetic diversity was quite low both at the species level (percentage of polymorphic bands (PPB) = 41.30%, Nei’s gene diversity (h) = 0.1331, and Shannon information index (I) = 0.2028) and the population level (PPB = 16.30-28.26%, h = 0.0496-0.1012, and I = 0.0756-0.1508). A high level of genetic differentiation among populations was detected based on Nei’s genetic diversity analysis (0.4344) and analysis of molecular variance (47.03%).