Satureja bachtiarica is a valuable medicinal plant that belongs to family Lamiaceae. In this research, genotypic and phenotypic variations among 57 individuals of this species were assessed based on three marker systems, namely, ISSR, RAPD and morphological traits. Principal component analysis showed that 75.91 % of the morphological variability was explained by all components for the studied individuals. Variables such as stem number, plant diameter, total weight, leaf and flower weight, stem weight, sepal length, petal length, petal tube length, sepal diameter, bracket length and bracket width were predominant in the first three components and contributed to most of the total variation. Leaf dimensions were in significant positive correlation with flower and inflorescence characteristics. Also, plant height showed significant positive correlation with characteristics related to inflorescence and weight. Clustering from morphological data allocated individuals into two main clusters with high variations. Profile patterns of 15 ISSR and 11 RAPD primers revealed 135 (98.78 %) and 84 (97.94 %) polymorphic fragments, respectively. The range of similarity coefficient by ISSR and RAPD markers were 0.08–0.63 and 0.09–0.69, respectively, indicating high genetic variation among individuals that originated from different geographic sites. UPGMA dendrograms based on ISSRs, RAPDs and ISSRs?RAPDs revealed high genetic diversity between studied individuals and grouped them into two main groups. Some cases of similarity and dissimilarity were observed between clustering based on ISSR and RAPD data. Also, the results showed that grouping based on molecular markers and morphological traits were different so these two systems could not discriminate individuals as the same way. The genetic relatedness among the studied individuals could provide useful information for conservation and selection of cross-parents in breeding.
