The levels of genetic variation in dioecious plant species have been reported to differ between male and female populations. This has been attributed to different factors including distribution patterns of individuals, sex ratio and also stochastic events. We measured the levels of genetic diversity in male and female populations of dioecious Pistacia atlantica (pistachio, Anacardiaceae) separately for each region and genders in two eco-geographically different regions over 350 km apart and of different population sizes in East Azerbaijan, Iran by randomly sampling 15 individuals of male and female from each of the regions using randomly amplified polymorphic DNAs. The percentage of polymorphic RAPD bands in the male populations of dioecious Pistacia atlantica was significantly higher (88.9%) than that of female populations (80.8%), and similarly, male populations had greater genetic diversity (0.387, Shannon; 0.252, Nei's) compared to female populations (0.381, Shannon; 0.249, Nei's). Genetic variation in larger population (Arasbaran) of P. atlantica (0.387, Nei's) was greater than that of the smaller (Jazire) population (0.312), indicating the impact of population size on genetic variation. Partitioning the total genetic variation using an analysis of molecular variance indicated that 77% of total genetic diversity was allocated within populations while 23% of this variation was dedicated among populations.