Pistachio is one of the most important horticultural products of Iran. The best way to get the maximum yield is to have genetically pure and monotonous gardens. Thereby, study of genetic variation and providing genetic identifications, make this possible to have homogenous gardens with high performance genotypes. In the present study, genetic diversity of 19 Iranian pistachio cultivars was assessed using ISSR and RAPD primers. Among these markers, RAPDs generated 127 amplification products, out of which 88 were polymorphic and ISSRs produced 114 amplification products, out of which 73 were polymorphic. RAPD fingerprinting detected more polymorphic loci (67%) than the ISSR (63%). Mean of polymorphism information content (PIC) for each of the marker systems (0.39 for RAPD and 0.39 for ISSR) suggested that both the marker systems were equally effective in determining polymorphisms. The dendrograms constructed using RAPD and ISSR marker systems were highly correlated with each other as revealed by high Mantel correlation (r= 0.83). These two marker systems were found to be useful for genetic diversity studies in pistachio and identify variation within Pistacia vera cultivars.