In order to assess the intra-cultivar genetic variation and the correlation between morphological traits of Akbari and Ahmadaghai cultivars of pistachio, 18 quantitative and 33 qualitative traits were measured and coded based on the pistachio descriptor. The results indicated that in this study, six main factors could contain 61.86 percent of the total variance. The fruit, nut, leaf, and terminal leaflet characteristics have constructed three main factor groups that compromise 76.60 percent of the total variance‏. These traits were the most important ones to separate 'Akbari' and 'Ahmadaghai' genotypes. Genotypes were divided into three groups based on six main factors. The first group contains the Ahmadaghai genotypes which significantly had the largest terminal leaflet width, fruit dimenstion (width and thickness), and nut thickness. The most genotypes of Akbari cultivar were located in the second group which is significantly different from other groups. These genotypes had the most fruit length and width. Also, the results showed that there was a wide variation in morphological traits of Akbari and Ahmadaghai cultivars which is due to provide of scions from trees that propagated from seed in the past.