The complete mitochondrial genome of the natural pentaploid loach Misgurnus anguillicaudatus is a circular molecule of 16,643 bp in size, containing 13 protein-coding genes, 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and two main noncoding regions (the control region and the origin of the light strand replication). Most of the genes are encoded on the heavy strand, except for ND6 and eight tRNAs. The control region is 918 bp in length and located between the tRNA(Pro) and tRNA(Phe) genes, some typical conserved elements (TAS, CSB1-3 and CSB D-F) were found in this region. All these features reflect a typical vertebrate mitochondrial gene arrangement of the pentaploid M. anguillicaudatus.