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Gentiana apiata N. E. Brown (Gentianaceae) is a perennial herb plant and only grows in Qinba Mountains in China. Here, we first characterized the complete nucleotide sequence of chloroplast (cp) genome of G. apiata via Illumina next generation sequencing platform. The complete chloroplast genome of G. apiata was 144,274 bp in length, comprising of a large single copy (LSC) region of 77,353 bp, a small single copy (SSC) region of 17,009 bp, and two inverted repeat regions (IRs) of 24,956 bp. The cp genome contains 127 genes, including 82 protein-coding genes, 35 tRNA, eight rRNA genes, and two pseudogenes. Phylogenetic analysis based on 18 cp genome sequences showed that G. apiata closely related to congeneric species.