The Glyptothorax fukiensis fukiensis is distributed widely in South China, e.g., Yangtze River, Pearl River, even Hainan Province, so it is a good model to study population genetics and historical biogeography. In this study, the complete mitochondrial genome sequence of G. fukiensis fukiensis has been obtained with PCR, which contains 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and a non-coding control region with the total length of 16,530 bp. The gene arrangement and composition are similar to most of other vertebrates. Most of the genes are encoded on heavy strand, except for eight tRNA and ND6 genes. Just like most other vertebrates, the bias of G and C has a universality in different statistics results. The complete mitochondrial genome sequence of G. fukiensis fukiensis is the first report for Sisoridae, it would contribute to better understand population genetics, biogeography, and evolution of this lineage.