The taxonomic and phylogenetic relationships within the genus Artemisia s.l. (Asteraceae) are controversial, and it has been considered 1 to 8 different genera. This work re-investigated the phylogenetic relationships in Artemisia using nuclear ribosomal (ITS) and chloroplast psbA-trnH DNA sequences using three sections of Artemisia, Dracunculus, and Serphidium. Three phylogenetic trees were conducted separately on the basis of ITS, psbA-trnH and combined sequences using maximum parsimony. The results showed that the three sections were clearly separated from each other, and that the heterogamous Dracunculus and Artemisia are closely related to each other than either to homogamous Serphidium. This may suggest the taxonomic importance of capitulum morphology in Artemisia s.l. Our data also cast doubt on the use of cytogenetic similarity e.g., basic chromosome number in grouping Serphidium and Artemisia s.s. Furthermore, AMOVA analysis showed a higher level of ITS (55.29%) and combined ITS+cppsbA-trnH (55.63%) variations among sections. This provides further evidence for separation of these three sections and supports the phylogenetic results. The higher ITS nucleotide differences detected in Artemisia (30.4737) compared to very low value in Dracunculus (2.3333) and Serphidium (1.23077) may propose that the Artemisia comprises of several incipient sections. This supports the previous suggestion that Artemisia is a complex group.