We sequenced chloroplast DNA from the matK, rbcL, and rpl16 regions to infer interrelationships within the pinyon pines (Pinus subsections Cembroides and Nelsoniae). Pinyons, together with subsections Balfourianae, Gerardianae, and Krempfianae have been classified in section Parrya, characterized by a dorsal umbo (raised area) on the ovulate cone scale. All three cpDNA regions support the separation of pinyon pines into subsection Cembroides and a monotypic subsection Nelsoniae and indicate that section Parrya is paraphyletic. We propose restricting section Parrya to the North American clade (subsections Cembroides, Nelsoniae, and Balfourianae) and transferring the Asian subsections Gerardianae and Krempfianae to section Quinquefolius (generally known as section Strobus). The data moderately support a sister relationship between subsections Nelsoniae and Balfourianae, rendering the pinyons paraphyletic. Several monophyletic groups can be identified within subsection Cembroides, including a sister relationship between P. maximartinezii and P. pinceana, which is at variance with morphological cladistic analyses. In general, relationships inferred from cpDNA are less consistent with morphological evidence than with internal transcribed spacer region data, despite paralogy in the latter marker.