Five new orchid species from southwestern China’s Yunnan Province and the Tibetan Autonomous Region, Neottia lihengiae, Neottia chawalongensis, Papilionanthe motuoensis, Gastrochilus lihengiae, and Gastrochilus bernhardtianus, are described and illustrated. To confirm their identities, and to resolve phylogenetic relationships, we sequenced the complete plastomes of these taxa with their congeneric species, adding new plastomes of three Neottia species, two Papilionanthe species and nine Gastrochilus species. Combined with published plastid sequences, our well-resolved phylogeny supported the alliance of N. lihengiae with the the N. grandiflora + N. pinetorum clade. Neottia chawalongensis is now sister to N. alternifolia, while P. motuoensis is closely related to P. subulata + P. teres. Conversely, phylogenetic analyses based on complete plastomes and plastid sequences showed inconsistent relationships among taxa in the genus Gastrochilus, but the two new species, G. lihengiae and G. bernhardtianus were supported by all datasets.