In this study, the whole mitochondrial genome of Elaphe schrenckii (Squamata: Colubridae) is first sequenced. It is a circular molecule of 17,165 bp in size and consists of 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes and 2 control regions (CRI and CRII). Except for eight tRNAs and ND6 gene, all other mitochondrial genes were encoded on the heavy strand (H strand). The gene order and orientation of E. schrenckii mitogenome are basically identical to that of other alethinophidian snakes. Mitochondrial genome analyses based on MP, ML and NJ yielded identical phylogenetic trees, indicating a close phylogenetic affinity of 12 species of Colubridae snakes. This study will facilitate the further research of the population genetics of this species and systematic analyses of the genus Elaphe.