Pinus subsection Ponderosae includes approximately 17 tree species distributed from western Canada to Nicaragua. We inferred phylogenetic relationships of multiple accessions for all widely recognized species from 3.7 kb of CpDNA sequence (matK, trnD-trnY-trnE spacer, chlN-ycf1 spacer, and ycf1). The sister relationship between subsections Ponderosae and Australes was corroborated with high branch support, and several clades, most with lower branch support, were identified within subsection Ponderosae. Pinus jeffreyi was sister to P. coulteri, P. sabiniana, and P. torreyana. Californian accessions of P. ponderosa and P. washoensis occurred in a clade separate from P. arizonica and P. scopulorum from the southwestern United States. Western Mexican species P. cooperi and P. durangensis had CpDNA sequences identical to one or more accessions of P. arizonica and P. scopulorum, and together these taxa were closely related to clades of P. engelmannii-P. devoniana (Mexico) and P. douglasiana-P. yecorensis-P. maximinoi (western Mexico to Guatemala). A well supported clade of taxa from Mexico and Central America included P. pseudostrobus, P. montezumae, P. hartwegii, P. maximinoi (one of three accessions), P. nubicola, and P. donnell-smithii. Chloroplast DNA sequences were nonmonophyletic for most species, although the degree of support varied.