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Gansu wapiti (Cervus elaphus kansuensis) is one of eight subspecies of wapiti in China, which has been placed under the second-ranked protected animals by Chinese government. No complete mitochondrial genomes of Gansu wapiti was determined until now, so the phylogenetic relationships among the subspecies of wapiti and other species of the genus Cervus have not been well studied. In this study, the complete mitochondrial genome of C. e. kansuensis was first sequenced and characterized. The genome is 16,430 bp in length, containing 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and one noncoding control region (CR). Maximum-Likelihood (ML) and Bayesian Inference (BI) trees based on the 13 PCGs show that C. e. kansuensis is clustered with other wapiti subspecies in China except for C. e. yarkandensis. It is also shown that Cervus elaphus is not a monophyletic group. This study provides important molecular evidence for the phylogenetic relationship among species in the genus Cervus. [ABSTRACT FROM AUTHOR]