The population genetic structure and genetic diversity of 90 individuals in three natural populations of Schisandra sphenanthera in Qinling Mountain were analysed based on ISSR molecular marker. Twelve inter-simple sequence repeat (ISSR) primers were used, 77 loci in which 65 were polymorphic and percentage of polymorphic loci was 85.71 %. Shannon′s information index (I) and index of gene diversity (H) were 0.507 and 0.348 by square root method,0.395 and 0.382 by Bayesian Method, respectively. This shows that there was abundant genetic diversity in Schisandra sphenanthera. Genetic differentiation coefficients were between 0.052 and 0.106(φST=0.106、FST=0.082、GST=0.066，θST=0.052), Gene flow (Nm) were between 2.108 and 4.558. The main genetic variation occurred within populations in Schisandra sphenanthera, the genetic differentiation among populations was very limited. The values of the genetic differentiation coefficients from different definitions were significantly dissimilarity. Therefore, they should not be used for comparison directly. The biological characteristics of Schisandra sphenanthera, such as dioecy, wind-pollination or insect-pollination, wide-area distribution, were the main reasons for the formation of genetic diversity.

Schisandra sphenanthera Rehd. et Wils.; genetic diversity; population genetic structure; inter-simple sequence repeat (ISSR); Qinling Mountain