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 A new orchid species, Bulbophyllum wolongense, from the Wolong National Nature Reserve (Sichuan, China), is proposed and described. Using the nuclear ribosomal DNA (nrDNA) and complete plastome sequences, we examined the phylogenetic position of this species and explored the plastome variation among the species of genus Bulbophyllum. The plastome of B. wolongense had a length of 157,496 bp and encoded 132 genes. Comparative plastid genome analysis revealed that the plastome length of B. wolongense was within the length range of other Bulbophyllum plastomes, and the plastome of B. wolongense was relatively conserved in structure compared to other Bulbophyllum plastomes that presented some genes (ndh, accD, and trnL-UAA) loss or pseudogenization, a small inversion, and inverted repeat boundary expansions. Furthermore, phylogenetic analyses of 17 Bulbophyllum whole plastomes, 67 shared protein-coding genes from 17 Bulbophyllum whole plastomes, and 4 DNA (ITS, Xdh, matK, and psbA-trnH) concatenated sequences from 127 Bulbophyllum species, all strongly supported that B. wolongense is a member of the Cirrhopetalum alliance and most likely in B. sect. Brachyantha. Further comparative morphological analysis showed that B. wolongense is clearly morphologically distinguishable from its closely related species in the phylogenetic tree.