Abstract:Mountain barriers was expected to interrupt habitats and have significant effects on the genetic structure,genetic biodiversity,and gene flow of plants.Using AFLP markers,we tested the genetic variation and differentiation of four populations of Cercidiphyllum japonicum Sieb.et Zucc.(Cercidiphyllaceae) along four riparian rivers in the northern and southern slopes of the Shennongjia region.The effect of the Shennongjia Mountain as a natural barrier to genetic structure and gene flow of the species was investigated.The Nei’s gene diversity (h) and Shannon index (I) were 0.116 and 0.173,respectively.Despite the low genetic differentiation between the two slopes (FST=0.075),the Neighbor-Joining Tree(NJ) and PCA data divided the four populations into two clusters corresponding to the northern and southern slopes.STRUCTURE analysis showed that the gene flow between populations within the same slope was higher than those in different slopes.Our results suggested that large mountains may have served as physical barriers to gene flow between plant populations.The low level of genetic differentiation of populations between the southern and northern slope may have resulted from the internal characters of long distance pollen and seed dispersal ability of the species.Our results suggested that large mountain may have served as physical barriers to gene flow between plant populations.