Estimation of genetic diversity and evaluation of plant germplasm is the most important step in collection and management of plant genetic resources. Also, comparison of different DNA-based genetic markers in diversity evaluation and then advising the most efficient markers is very important. In order to investigate genetic variation among Persian oak (Quercus brantii Lindi.) populations of Lorestan province (Iran), 20 genotypes were collected from different geographical and climatic regions. After DNA extraction, polymerase chain reactions (PCR) were used for study of polymorphism using three markers including ISJ, ISSR and SCoT. Genotyping was performed using the polymorphic bands obtained from all three markers separately, and also by combining the data of three markers. PCR results of the primers showed 91 polymorphic bands with an average of 71% per locus. The ISSR marker with 44 bands had the most polymorphic bands. Genotypes were discriminated by ISJ, ISSR and SCoT markers in 5, 6 and 5 groups, respectively, and using the combined data of three markers, genotypes were classified in 5 groups (each group included more than one genotype) and 3 group (each group included one genotype).  The results showed that the obtained clustering by different markers were nearly consistent with clustering of genotypes based on the climatic origin of genotypes. The most similarity between the groupings was between ISJ and ISSR markers with 89%. Overall, the results indicated the usefulness of markers used to estimate genetic distances between different oak communities.