Chloroplast DNA restriction site variation was used to examine phylogenetic relationships in Artemisia sect. Tridentatae, a complex of eleven species of woody shrubs dominant in the sagebrush communities of western North America. Twenty-seven endonucleases were utilized, and resulted in 82 variable site mutations, 27 of which were phylogenetically informative. The resulting cpDNA phylogeny indicates that sect. Tridentatae is monophyletic, with the exclusion of A. palmeri and the inclusion of A. bigelovii. A sister-group relationship between A. palmeri and three members of subg. Artemisia supports the exclusion of A. palmeri from sect. Tridentatae, and its inclusion within subg. Artemisia. Artemisia bigelovii, an anomalous species with heterogamous capitula, occurs within the Tridentatae clade, supporting its inclusion within the section. Introgression and subsequent chloroplast capture of the Tridentatae genome by A. californica and A. filifolia may explain the unexpected placement of these two species in the Tridentatae clade. Low cpDNA sequence divergence provides only limited resolution of phylogenetic relationships within sect. Tridentatae, indicative of a recently differentiated and/or hybridizing polymorphic species complex. In addition, the cpDNA data provides only equivocal evidence for either of two hypotheses regarding the origin and phylogenetic relationship of sect. Tridentatae within Artemisia.