Salvia limbata is one of the aromatic herbs of Lamiaceae that naturally grows in different regions of Iran. This species has several usages in folk and modern medicine. In the current research, population genetic divergence and structure were evaluated in eight Iranian populations of this species. Nuclear genomes were extracted using CTAB method and amplified by ten ISSR primers. Parameters of genetic divergence changed among and within the examined populations. Percentage of among populations polymorphism was higher than within population ones in most of studied populations. It was supported by results of Analysis of Molecular Variance test, which revealed the large part of significant genetic variation belonged to among populations rather than within populations. In this regard, individuals of most populations were close together, while according to UPGMA tree, the studied populations were clustered into seven groups. STRUCTURE analysis and NJ tree produced similar results. The low rate of gene flow (Lm) and highest value of genetic differentiation (GST) confirmed the high genetic differentiation of the studied populations. Popart analysis revealed the occurrence of several mutations in order to adapt populations with environmental conditions. The occurrence of adaptive mutations and gene flow disruption due to habitat separation seems to differentiate the populations.
