Zelkova carpinifolia (Pall.) C. Koch is an ancient tree of Ulmaceae family, which considered as an important species in Hyrcanian forests of Iran. We examined infraspecific genetic variation and population structure in this species by SCoT molecular markers. Five individuals were harvested from 10 populations and their nuclear genomes were extracted by C-TAB modified protocol and amplified using 10 SCoT molecular primers. We used GenAlex, PopGene, GenoDive and Structure software for statistical analyses. Results of AMOVA test indicated a great proportion of genetic diversity assigned to among populations. In addition, the large amounts of Ht and Gst indicated a strong genetic differentiation that were resulted from a flat rate of gene flow. We recorded a significant correlation between genetic diversity and geographic distance by the Mantel test. TCS networking indicated a low rate of mutation occurred among the individuals of most species. According to UPGMA tree and structure analyses, two main groups of genotype were detected that were in accordance with their geographical distribution. The genetic structure of both genotypes were nearly uniform, however some intermediated genetic
