Pistachio is one of the most important horticultural crops in Iran. Selection of suitable genotypes, resistant to unfavorable environmental and soil conditions and diseases, are important for increasing yield efficiency and the acreage of this important crop. The aim of this research was to evaluate wild pistachio species and genotypes native to Iran and also to determine any relationships that exist according to their phenotypical characteristics. A total of 11 pistachio types in situ from Kerman and Fars provinces and ex situ from the Iranian Pistachio Research Institute (IPRI) were used during the research. Thirty-one morphological characteristics (17 quantitative and 14 qualitative) were evaluated based on the pistachio descriptor (IPGRI). Results from simple correlation analyses showed significant positive and negative correlations in certain important characteristics. Nut thickness and weight were in significant correlation with the size (dimensions) of the leaves and terminal leaflets. Factor analysis was used to determine the effective characteristics and the number of main factors. For each factor loading a value of more than 0.65 was judged as being significant. Effective characteristics were categorized into seven main factors that contributed to 94% of the overall variance. Leaf and nut characteristics were defined mainly by the first factor contributing to 40% of the total variance. Pistachio genotypes were clustered based on seven factors and at a similarity distance of 10, these were further divided into three sub-clusters each consisting of genotypes belonging to species P. vera L., P. khinjuk Stocks. and P. atlantica Desf. Based on the results, P. khinjuk was located between the other two species, but resembled P. atlantica more than P. vera.