Genetic variability, phylogenetic relationship and population structure were evaluated among 50 accessions of three Iranian Pistacia species using start codon targeted (SCoT) primers and morphological traits. Genetic similarity and structure of the germplasm were evaluated based on the molecular data and their association with phenotypic characters were estimated by multiple regression analysis. The SCoT primers amplified 76 fragments on the germplasm with high level of polymorphism (98.46%). The average of RP, PIC, and MI were 3.30, 0.38, and 2.12, respectively representing the effectiveness of primer set for genetic discrimination among the Pistacia species. A high level of genetic variability was observed among the accessions. The germplasm belonging to the same species were grouped together using different clustering methods. Among the studied species, P. khinjuk Stocks. proved to be the most diverse species and had the highest gene diversity (h = 0.33) and Shannon’s information indices (I = 0.483) followed by P. atlantica Desf. and P. vera L., respectively. According to results, P. vera and P. khinjuk were the most closely related species, while P. atlantica and P. vera had the highest genetic differentiation. Significant association was observed between some of the morphological attributes and a number of SCoT generated fragments. Three species-specific amplicons were detected in P. atlantica and P. vera which can be used for designing sequence characterized amplification regions (SCAR) primers and subsequent marker assistant selection as well as species assignment in controversial cases. This study indicates the effectiveness of SCoT technique for genetic characterization of Pistacia germplasm, which could be used for genetic diversity and evolutionary assessments, detecting and tagging of agronomically important traits as well as quick, reliable and more precise authentication of Pistacia species.

 使用起始密码子靶向（SCoT）引物和形态学特征，对三种伊朗黄连木属物种的50个种之间的遗传变异性，系统发育关系和种群结构进行了评估 。根据分子数据评估种质的遗传相似性和结构，并通过多元回归分析估计它们与表型性状的关联。SCoT引物在种质上扩增出76个片段，具有较高的多态性（98.46％）。RP，PIC和MI的平均值分别为3.30、0.38和2.12，分别代表引物组对黄连木遗传歧视的有效性。  种类。在这些种之间观察到高水平的遗传变异性。属于同一物种的种质使用不同的聚类方法分组在一起。在研究的物种中，  P。khinjuk 种群。被证明是最多样化的物种，并且具有最高的基因多样性（h  = 0.33），香农的信息指数（I  = 0.483）紧随其后是 P. atlantica  Desf。和 P. vera L.。根据结果，  P.芦荟 和 P. khinjuk 是最密切相关的物种，而 P.大西洋 和 P.症 遗传分化最高。在某些形态属性和许多SCoT生成的片段之间观察到显着的关联。在大西洋假单胞菌 和 阿拉伯假单胞菌中检测到三个物种特异性扩增子  ，可用于设计序列特征扩增区域（SCAR）引物和随后的标记辅助选择，以及在有争议的情况下进行物种分配。这项研究表明SCoT技术对黄连木 种质遗传特征的有效性， 可用于遗传多样性和进化评估，农学重要性状的检测和标记以及对黄连木的快速，可靠和更精确的鉴定  种类。