The nuclear ribosomal internal transcribed spacer and chloroplast rbcL-accD intergenic spacer regions of species in the Pungentes subsection of Chorizanthe (spineflower) were analyzed. The goals of the study were to ascertain the phylogenetic relationships of taxa in the C. pungens-C. robusta complex to each other and to the other Pungentes species. The ITS phylogenies showed that C. diffusa was most distant from the other species and that C. cuspidata, C. pungens and C. robusta were not monophyletic. The four varieties of the C. pungens-C. robusta complex resolved into montane and coastal groups but the groupings were not in agreement with current classification. Statistical parsimony analysis divided 26 chloroplast DNA haplotypes into four groups with the 18 sampled populations of the C. pungens-C. robusta complex displaying a high degree of phylogeographic structure despite some incomplete lineage sorting. The haplotype analysis was not discordant with the ITS phylogeny. Possible taxonomic revisions and implications for conservation and management are discussed.