The Artemisia genus is a group of valuable medicinal plants that are found in the temperate regions of the world. These plants have many pharmacological benefts. Iran is known to be one of the main centers of distribution for various Artemisia species, however, there is limited information available about their genetic diversity and population structure at the molecular level. In this study, 50 Artemisia accessions belonging to fve species (A. fragrans Wild., A. absinthium L., A. scoparia Waldst. & Kit., A. biennis Rchb., and A. annua L.) were evaluated for genetic diversity and population structure using several start codon-targeted polymorphism (SCoT) and CATT-box derived polymorphism (CBDP) markers. Ten SCoT and eight CBDP primers were used, yielding 69 and 77 fragments, respectively. Out of these fragments, 63 and 64 were found to be polymorphic. The results showed that the CBDP marker technique was more efcient compared to SCoT due to higher values of informativeness indices. An analysis of molecular variance (AMOVA) based on all two markers and combined data revealed a higher distribution of genetic variation among species. Furthermore, A. absinthium species showed a high level of genetic diversity due to the maximum values for genetic variation parameters. Hence, this species can be attended to in future genetic and metabolomics research. The obtained clustering patterns of studied accessions by all molecular data were similar to each other and were further supported by the principal coordinate analysis (PCoA). All investigated accessions were grouped into fve separate clusters. In conclusion, the results of this study suggest that SCoT and CBDP markers can be suitable for use in fne mapping research because they are more efcient for the detection of genetic polymorphism in Artemisia germplasm.
