Zelkova carpinifolia (Pall.) C. Koch is an ancient tree of the Ulmaceae family, which is considered an essential species in the Hyrcanian forests of Iran. Therefore, we examined infraspecific genetic variation and morphological polymorphism in ten Iranian populations of this species. For the molecular study, nuclear genomes of 50 individuals of 10 populations were extracted by C-TAB modified protocol and amplified using 10 SCoT molecular primers. Additionally, 10 individuals were selected per population for morphometric analyses. We used SPSS, GenAlex, PopGene, GenoDive, and Structure software for statistical analyses. All quantitative morphological characteristics differed among and within the populations. Meanwhile, the ANOVA test showed a significant difference (P B 0.05) for a few traits. Significant correlations were determined between some morphological traits with geographic parameters of habitats. No significant correlation was detected between morphological variation and geographic distance by the Mantel test. However, some qualitative features such as leaves margin, basal forms, and blade shape differed among and within the populations. The UPGMA dendrogram revealed a high level of morphological polymorphism within populations, followed by a low level of among populations morphological differentiation. However, we detected four morphotype groups among the evaluated populations. Results of the AMOVA test indicated a significant proportion of genetic diversity among the populations. The large amounts of HT and GST showed a strong genetic differentiation created by a flat rate of gene flow. Moreover, isolation by distance occurred among the populations. TCS networking indicated a low rate of mutation occurred among the individuals of most populations. According to UPGMA tree and structure analyses, two main groups of genotype were detected that were in accordance with geographical distribution of the populations. In addition, a large amount enetic dissimilarity was detected between some populations. The genetic structure of both notypes was nearly uniform; however, some intermediated were observed. We observed some significant correlations between various genetic diversity parameters with some leaf morphological features, which indicates genetic base of these ariations. For some populations, the clustering patterns were similar for both, morphology and genetic diversity, studies. The results of morphological study did not support the existence of subspecies in Z. carpinifolia, while results of molecular study were entirely different. Our findings revealed that genetic isolation by distance, a flat rate of gene flow, a low mutation level, genetic drift, and vegetative reproduction lead to a substantial population genetic differentiation, followed by a small amount of within-population genetic diversity. However, the relative uniformity in environmental condition resulted in similar phenotypic plasticity between some populations, which was supported by correlation analysis.
