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Abies ziyuanensis is critically endangered and endemic to Guangxi and Hunan provinces of China, with no more than 600 surviving individuals. In this study, we reported the complete chloroplast (cp) genome of A. ziyuanensis. The complete chloroplast genome is 121,274 bp in size. In total, 114 genes were identified, including 68 peptide-encoding genes, 35 tRNA genes, four rRNA genes, six open reading frames, and one pseudogene. Thirteen genes contain introns. In phylogenetic analysis, the tree supported the monophyly of the genus Abies. The complete plastome of A. ziyuanensis will provide potential genetic resources for further conservation and evolutionary studies of this highly endangered species.