In this study, a complete mitochondrial genome of a female Harpiocephalus harpia from Zhejiang Province, China, was sequenced using Illumina Hiseq. The genome is 16,400 bp in length, containing 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes, and a control region. Most of the genes were encoded on the H-strand, except for 8 tRNA and ND6 genes. Phylogenetic tree using maximum likelihood suggests H. harpia is sister taxon to Murina. The complete mitochondrial genome herein provides basic information for future taxonomic and phylogenetic studies.