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Vanilla shenzhenica Z.J.Liu & S.C.Chen is a new species of orchid found in Shenzhen, South China for the first time. Here we report the complete chloroplast (cp) genome sequence and the features of V. shenzhenica. Its cp genome sequence was 151,537 bp, including one large single-copy region (LSC, 87,487 bp), one small single-copy region (SSC, 19,172 bp), and two inverted repeat regions (IRs, 22,439 bp). It encoded 123 genes, of which 104 were unique genes (69 protein-coding genes, 31 tRNAs and 4 rRNAs). The phylogenetic relationships show that V. shenzhenica is sister with V. aphylla.