Abstract Pistacia atlantica Desf. mutica and Pistacia khinjuk are dioecious plants. In addition to having a high nutritional and medical value, they are important Pistacia vera rootstocks. Quick gender identification in juvenile stage would result in great saving in time and cost. With respect to the long juvenile stage of Pistacia species, marker assistance selection can facilitated breeding, Sequence Characterized Amplified Region (SCAR) was used to determine sex in these two wild species. According to the results, a 297 bp fragment was amplified in all female trees which was absent in male trees. Although sex determination in Pistacia is still unknown, correlations between the SCAR marker and sex locus in Pistacia species, sex determination in Pistacia species is possibly controlled by a single or a few loci in this genus. Consequently by using SCAR PCR technique, it is possible to detect sexual phenotype of Pistacia atlantica Desf. mutica and Pistacia khinjuk at the early juvenile stage.

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