Abstract Genetic diversity can play a key role in the survival of plant species. In the present study, the first data on genetic diversity and structure of nine populations in Quercus libani G. Olivier collected from northwest of Iran was provided using inter-simple sequence repeat (ISSR), interretrotransposon amplified polymorphism (IRAP), and start codon targeted (SCoT) markers. The proportions of polymorphic bands were 94.54, 97.96, and 90.86 %, detected by 18 ISSR, 10 IRAP, and 10 SCoT primers, respectively. The mean of Nei’s gene diversity index (H) among the populations by ISSR, IRAP, and SCoTwas 0.16, 0.19, and 0.19, and Shannon diversity index (I) was 0.25, 0.29, and 0.28, respectively. Partitioning of genetic variability by analysis of molecular variance (AMOVA) according to each marker and combined data revealed that the intra-population genetic diversity was higher than among populations. Cophenetic correlation coefficient values were statistically significant between ISSR and SCoT, while it was low and insignificant between IRAP and ISSR and between IRAP and SCoT. The dendrogram obtained by each marker and combined dataset reflected geographic structure among most of the populations. Regarding the differentiation among the studied populations and the complexity in taxonomic situation within Q. libani, inter-specific crossings and/or the presence of more than one species within Q. libani is possible. This genetic characterization of Q. libani from Iran contributes to knowledge of the genetic structure of the species and is valuable to define strategies for conservation.
