The complete mitochondrial genome sequence of the Shaping horned toad Megophrys shapingensis, the first complete mitogenome from the family Megophryidae, was determined. The total length of this complete mitogenome was 17,631 bp, containing 13 protein-coding genes, 2 rRNA genes, 22 tRNA genes, and a control region (D-loop). The gene arrangement and composition of the mitogenome were similar to those of most amphibians. The base composition on light strand was 28.2% A, 31.5% T, 26.1% C, and 14.3% G. The D-loop region contained 10 copies of 97-bp tandem repeats. The complete mitogenome sequence of M. shapingensis provided fundamental data for resolving phylogenetic and genetic problems related to this species.