The genus Pistacia is a member of the Anacardiaceae family and consists of at least 11 species. Pistacia species are dioecious and wind-pollinated trees. Among these species, Pistacia vera (Pistachio) has edible nuts and economically important species. The other species usually grow wild and are used as rootstock for P. vera. P. vera is native to north Afghanistan, northeast Iran and central Asian republics. Pistachio is an important horticultural and economical plant whose cultivation and production has a long history in Iran and the country is well known internationally for this interprise. Iran has been considered as one of the origins of this plant. The systematic position and intrageneric relationships of Pistacia species are controversial, therefore precise genetic relationships among cultivars and species using molecular DNA markers is necessary to make better breeding programs. Chloroplast DNA (cpDNA) has been used extensively to analyse plant phylogenies at different taxonomic levels because of conservative size, organization and sequence. Thus, in this study in order to investigate the evolutionary trend of the genus Pistacia , by using the plastid trnC-trnD and atpB-rbcL. In this study plant material from commercially grown Pistachio cultivars was collected from four different countries including Iran, Syria, Turkey and United States of America. Trn C-trnD region was amplified with three pairs of specific primers. The PCR products ligated into T-vector and then transferred into E.coli (MC1061 strain) with three method: Cloning kit, Electroporation and Calcium Clorid. Clonies containing our fragments were selected by Colony PCR and Digestion procedures. After sequencing, three microsatellites were recognized in trnC-trnD region and primer design from flanking region of the reapeats could introduce chloroplast microsatellite in Pistacia species. The combined plastid data sets were analysed using MEGA4 software with maximum composite likelihood method. Based on the data sets derived from the two regions of trnC-trnD and atpB-rbcL, wild genotypes were separated from P.vera (cultivated species) including cultivated genotypes from different countries and clustered in one group. Clustering of Sarakhs with cultivated genotypes might be an indication that Sarakhs has contributed to the development of cultivated varieties. In addition, close relationship between Iranian cultivars and foreign types strengthen the presumption that Ira is one of the two major centres of Pistacia diversity and the origin of this genus. cluster analysis indicated that P.khinjuk and Baneh have a closer relationship than P.vera . According to the dendrogram, P. lentiscus that is a evergreen species was grouped in a separated
