Balsamorhiza and Wyethia together comprise 24 species native to western North America. All species in the two genera are perennial herbs with large taproots and chromosome base numbers of x  =  19. The species of Balsamorhiza have exclusively basal leaves while the species of Wyethia have cauline leaves (in addition to basal leaves in some species). The relationships among the species of Balsamorhiza and Wyethia were examined using sequences from the nuclear internal transcribed spacer and external transcribed spacer regions and the chloroplast 3′ trnK intron. Twenty-three species of Balsamorhiza and Wyethia and eight outgroups were sampled. The analyses support the monophyly of the Balsamorhiza/Wyethia clade. Wyethia ovata, a species from southern California and northern Baja California, is sister to the other members of the Balsamorhiza/Wyethia clade. Balsamorhiza is strongly supported as monophyletic and is the sister to the rest of Wyethia. The mostly Californian Wyethia section Agnorhiza, which lacks basal leaves, is not monophyletic. The remainder of the Wyethia species, traditionally placed in sections Alarconia and Wyethia, form a clade in the molecular trees and share synapomorphic large basal leaves.