Pistachio is economically important in Iran. Selection of suitable rootstocks, resistant to unfavorable and soil conditions and diseases, is important for increasing yield and the acreage of this crop. It is essential to identify the genetic relationships among Pistacia species for the breeding of pistachio rootstocks. The goal of this study was to determine the genetic relationship among Pistacia species (P. vera L., P. khinjuk Stocks., P. eurycarpa Yalt., P. atlantica subsp. atlantica Zoh., P. atlantica subsp. mutica Fish et C.A. Mey and P. atlantica subsp. cabulica Stocks.) with potential in the breeding of rootstocks using the selective amplification of microsatellite polymorphic loci (SAMPL) technique. Six primer combinations produced a total of 182 bands, with an average of 30.33 bands per primer pair, of which 128 were polymorphic. Three branches were obtained, the first containing P. vera, and the second containing P. khinjuk, P. eurycarpa, P. atlantica and subspecies mutica and cabulica, with numerous leaflets clustered in the third branch. UPGMA analysis separated P. atlantica subspecies from P. eurycarpa.