Members of Artemisia (Asteraceae) are of great economic, ethnobotanical and medicinal importance. There are about 500 species distributed throughout the world except for Antarctica. Morphological, anatomical, cytological, palynological, genomic and physiological techniques are being used from ancient times for identification and natural classification of these plants but still have restrictions. The current study will help out in resolving the taxonomic complexities of the genus Artemisia sensu lato with an emphasis on subgenus Seriphidium sensu stricto and point out the potential molecular taxonomic markers. Artemisia subg. Seriphidium is one of the largest groups within Artemisia, encompassing more than one hundred species, some of them having considerable ecological and economical importance. However, the evolution of subg. Seriphidium has received less attention in comparison to other subgenera of Artemisia, probably, apart from the difficulty of sampling throughout its very large distribution area, because of the low molecular and morphological variability observed in previous studies. Here, thorough taxonomic sampling within both Artemisia and subg. Seriphidium is used to reconstruct the evolutionary history of the subgenus, employing nuclear and plastid DNA sequences as well as various phylogenetic, biogeographic and diversification dynamics tools to analyze the data. The results show that subg. Seriphidium is not monophyletic but segregated into two main clades: one large monophyletic group corresponding to the formerly recognized sect. Seriphidium and a second, small clade, phylogenetically distant from the first. Biogeographic and diversification analyses indicate that rapid radiation of species within the sect. Seriphidium occurred in Central Asia during the Miocene-Pliocene transition. The results of our biogeographic analysis suggest that this diversification process started around the Tian-Shan, Pamir and Hindu Kush mountain ranges, subsequently expanding into the Eurasian continent. Finally, the study uncovered numerous incongruences between taxonomic and genetic information in several sect. Seriphidium species, which could be explained by morphological uniformity, hybridization and/or incomplete lineage sorting processes. Moreover, the study researches the systematic position of members of Artemisia from Pakistan using molecular data. Furthermore, the research strongly supported the inclusion of Seriphidium within Artemisia. More investigation encompassing extensive sampling from numerous biogeographic regions and markers that are more variable would be necessary to disentangle systematic affinities within the genus.