There are four species of Artemisia known in Ethiopia, namely A. schimperi (endemic), A. abyssinica, A. afra and A. absinthium (syn. A. rehan). All these species occurred naturally except A. absinthium, which usually grows in private gardens. The main objective of this study was to reconstruct the molecular phylogeny to determine phylogenetic positions of Ethiopian Artemisia species using the external and internal transcribed spacers (ETS, ITS). A total of 57 sequences (nine new and 48 retrieved from GenBank) were used in maximum parsimony (MP) and maximum likelihood (ML) analyses. The Ethiopian Artemisia species were recovered in three clades corresponding to subgenera (Artemisia, Absinthium and Pacifica). The sequences of Ethiopian A. absinthium (previously known as A. rehan) grouped with A. judaica and are distantly related to the European A. absinthium. Artemisia abyssinica and A. schimperi have affinities to A. subg. Pacifica with adaptations to a relatively cool and dry subalpine tropical climate.