AbstractAbies ernestiivar.salouenensis(Bordères & Gaussen) W. C. Cheng & L. K. Fu is endemic to southwest China, including the southeastern Tibetan Plateau and the northwestern Yunnan Province. The taxonomic relationships betweenA. ernestii var. salouenensisand two other closely related fir species (A. chensiensisTiegh. andA. ernestiiRehd.) still need to be determined. Here, we report for the first time the whole chloroplast genome ofA. ernestiivar.salouenensis. Its genome is 121,759 bp long and is characterized by a circular structure with 68 peptide-encoding genes, 16 tRNAs, six ORFs, and four rRNAs. We also identified 70 microsatellite repeat sequences and 14 tandem repeat sequences in the chloroplast genome ofA. ernestiivar.salouenensis. Comparative genome analysis indicated considerable variation inycf1 andycf2. Phylogenetic analysis supported the monophyly ofA. ernestiivar.salouenensis,A. chensiensisTiegh., andA. ernestiiRehd. The relationships among them should be surveyed using more samples at the species level. This study will facilitate taxonomic studies and the development of suitable chloroplast markers for fir species.