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The Hong Kong Dwarf Snake Calamaria septentrionalis Boulenger, 1890 is widely distributed in south of China and North of Vietnam. The complete mitochondrial genome (mitogenome) sequence of C. septentrionalis was determined by shotgun sequencing. The mitogenome of C. septentrionalis is 17,053 bp in length and contains two ribosome RNA genes, 13 protein-coding genes, 22 tRNA genes, and two noncoding regions. Most genes of C. septentrionalis were distributed on the H-strand, except for the ND6 subunit gene and eight tRNA genes which were encoded on the L-strand. The phylogenetic tree of C. septentrionalis and 15 other related species was built. The DNA data presented here will be useful to study the evolutionary relationships and genetic diversity of C. septentrionalis. [ABSTRACT FROM AUTHOR]