Background Salvia macrosiphon is an aromatic perennial species of Lamiaceae family that grows naturally in different parts of Iran. This herb is widely used in folk and modern medicine. Although in Flora Iranica and Flora of Iran, no infraspecific taxonomic rank has been detected for S. macrosiphon, some infraspecific taxonomic ranks have been reported. In the current study, we evaluated the genetic diversity and structure of 11 populations of this species to detect inter and intrapopulation genetic diversity and to survey the possibility of infraspecific taxonomic ranks in this species. Methods and results We utilized the modified C-TAB protocol for DNA extraction and amplified the genomes using several SCoT molecular markers. We calculated of genetic diversity and polymorphism parameters using GenAlex 6.4, Geno–Dive ver.2, PopGene, PopART and Structure 2.3.4. The parameters of genetic polymorphism differed between the populations. Moreover, a low rate of gene flow supported a moderate level of population’s genetic diversity and differentiation. According to haplotypes network (TCS) analysis, a high level of genetic mutation has occurred among the individuals of some populations leading to high intrapopulation diversity. On the basis of structure analysis and Nei’s genetic distance, the examined populations were classified into four genotypes. Conclusions The clustering pattern of the populations in each group was not related to geographical distance or phytogeography. It seems that the wide geographic distribution, a small gene flow rate and the occurrence of a high level of genetic mutation lead to infraspecific genetic differentiation in the species and we suppose some infraspecific ranks exist for it.
