Abstract:By using inter-simple sequence repeat (ISSR) markers technique, this paper studied the genetic diversity of ten populations of endangered relic shrub Sinocalycanthus chinensis. The results showed that at species level, the percent age of polymorphic loci (P) was 73.08%, Shannon’s in- dex (h) was 0.3097, and Nei’s gene diversity (I) was 0.1987, indicating a high level of genetic diversity, but at population level, they were 23.65%, 0.1251 and 0.0839, respectively, suggesting a low level of genetic diversity. The analysis of molecular variance (AMOVA) demonstrated that there was a relatively high level (57.11%) genetic variation among the populations, with the gene differentiation coefficient (Gst) and gene flow being 0.5779 and 0.3651, respectively. The high genetic differentiation among populations and the low genetic diversity within populations could be attributed to the habitat fragmentation and the limited gene flow among populations. Through cluster analysis, the ten populations of S. chinensis were classified into two groups, with the eight populations in Lin’an City forming a group and other two in Tiantai County forming another group.