Stachys lavandulifolia Vahl. (Lamiaceae) is an important medicinal plant that grows in different parts of Iran and forms many geographical populations. We have no information on its population genetic structure, genetic diversity, and morphological variability in Iran. Therefore, we planned a genetic and morphological investigation in St. lavandulifolia geographical populations in Iran. The obtained data are important for conservation and germplasm management of this medicinal plant species. Seventy-four plants were randomly collected from 14 geographical populations and studied for genetic diversity (ISSR molecular markers) and morphological variability. The highest value for gene diversity occurred in populations 1 and 4 (0.133 and 0.129, respectively). The latitude and altitude were positively correlated with gene diversity and genetic polymorphism while longitude was negatively correlated with them. The Mantel test showed correlation between genetic distance and geographical distance. AMOVA revealed a significant genetic difference among populations and showed that 58% of total genetic variation was due to within-population diversity. The STRUCTURE analysis and K-Means clustering identified two gene pools for St. lavandulifolia. The consensus tree of both molecular and morphological data identified divergent populations.
