The genetic diversity of a large number of pistachio genotypes grown in Iran is not exactly known. Most of the studies on genetic diversity of Iranian pistachio varieties are based on morphological characteristics or isozyme markers. In the present study, the genetic diversity of selected pistachio cultivars along with some wild species were evaluated by Amplified Fragment Length Polymorphism (AFLP) markers. 13 AFLP primers were used for evaluation of 45 pistachio genotypes. Totally, 506 polymorphic bands with an average polymorphism of 95.2% were detected. Cluster analysis assigned pistachio genotypes into 4 groups. All commercially cultivated pistachios were clustered in group I and II. The wild pistachio genotypes were separated from the cultivated ones. These data demonstrate that AFLP is a reliable tool for analyzing pistachio genetic diversity.