PERSIAN oak (Quercus brantii Lindl.) is a common woody species in the Zagros forests of Iran. The current study evaluates the variation among the Q. brantii populations in the southwestern forests of Iran using amplified fragment length polymorphism (AFLP) and leaf morphology. A total of 135 trees were sampled from 27 populations representing nine regions in the provinces of Khuzestan (GOL, EMA, BAB, MOG, ALG), Chaharmahal and Bakhtiari (MON), Lorestan (KHA), Kohgiluyeh and Boyer-Ahmad (DIS) and Fars (BAA). Twelve morphological leaf traits were analyzed using PCA and Ward's clustering methods. The results of ANOVA showed significant differences between populations, but the PCA graph and clustering analysis could not separate the populations on the basis of leaf characteristics. An analysis of molecular variance indicated that most genetic variation was contained within populations (95%); differences between populations accounted for only 1% and 4% was attributed to variation between regions. The five regions of Khuzestan have similar genetic structures. This was observed for the regions in Fars, Lorestan and Chaharmahal and Bakhtiari. Region DIS of Kohgiluyeh and Boyer-Ahmad had a separate genetic structure. The Dendrogram of Quercus brantii populations based on AFLP marker and Cluster analysis of populations using Ward's method based on morphological data don't confirm each other and in both, populations mix together. The current study revealed the some morphological and molecular differences in some populations of Persian oak in Iran. Population genetic information can provide critical insights into range expansion and evolutionary potential to adapt to environmental changes.