Ziziphora clinopodioides Lam., (Lamiaceae), is a perennial herb which is used as traditional medicine in Iran. Different authors disagree on the number of subspecies. In general, taxonomic and biosystematic studies of Ziziphora clinopodioides have been limited and no molecular phylogenetic or biogeographic study of the species has been carried out. Therefore, the aims of this study were (1) to determine the number of subspecies, (2) to produce information on the species’ genetic structure and intra-specific genetic variability, and (3) to produce data on the probable date of appearance of Ziziphora clinopodioides in Iran. We used a combination of morphological and molecular data to study plants randomly collected from 5 geographical regions. Both analyses revealed a high level of within population variability and grouping of the studied provinces produced an admixture that indicated the absence of any subspecies within the species. STRUCTURE analysis and K-Means clustering identified two gene pools within the country. The probable date of divergence obtained was 5-10 Mya for the appearance of this species in the mountainous regions of Qazvin and Mazandaran.
