A phylogeny of Cantua was estimated using parsimony analyses of DNA sequences from the nuclear ribosomal ITS region and the cpDNA spacers trnT-tmL, tmL-trnF, and partial ndhF coding region. One of the two species formerly included in Huthia was included in these analyses; the other is known only from the type. Data from the phylogenetic analyses strongly supported the paraphyly of Cantua to this taxon, Cantua volcanica (= Huthia coerulea). This result supports the earlier inclusion of the two species formerly placed in Huthia within Cantua. Cantua volcanica was most closely related to C. quercifolia and these two species together were the sister group to the rest of Cantua. The remaining taxa, C. flexuosa, C. cuzcoensis, C. bicolor, C. candelilla, C. buxifolia, and C. pyrifolia were well supported as a monophyletic group. For most species, multiple individuals were sampled. In each case, except for the individuals of C. buxifolia, the multiple individuals formed a clade. Precise relationships between C. buxifolia and other species remain unresolved. Cantua mediamnis (= Huthia longiflora) and C. dendritica were not included in the phylogenetic analyses, however based on morphological characters the former is clearly allied with C. volcanica and the latter with C. flexuosa.