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The first complete chloroplast (cp) genome of the Chinese endemic and endangered species, Magnolia omeiensis, were reported in this study. The M. omeiensis cp genome was 160,091 bp in length, with two inverted repeat (IR) regions of 26,584 bp, one large single-copy (LSC) region of 88,160 bp, and one small single-copy (SSC) region of 18,763 bp. The cp genome of this species contained 113 unique genes, including 79 protein-coding genes, four ribosomal RNA, and 30 transfer RNA genes. The overall GC content was 39.3%. Phylogenetic analysis of 24 representative cp genomes within the genus Magnolia suggested M. omeiensis is closely related to M. yunnanensis.