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Abies yuanbaoshanensis is critically endangered and endemic to Guangxi province of China, with no more than 900 surviving individuals. In this study, we reported the complete chloroplast (cp) genome of A. yuanbaoshanensis. The complete chloroplast genome is 121897 bp in size. In total, 112 genes were identified, including 74 protein-coding genes, 34tRNA genes, and four rRNA genes. In phylogenetic analysis, the tree supported the monophyly of the genus Abies. The complete plastome of A. yuanbaoshanensis will provide potential genetic resources for further conservation and evolutionary studies of this highly endangered species.