Pseudopleuronectes herzensteini belonging to Pleuronectiformes (family Pleuronectidae) is important in the fishery industry. However, the molecular biology of this valuable fish has hardly been reported. Thus, here we report the complete mitochondrial genome of P. herzensteini. The mitochondrial DNA (mtDNA) of P. herzensteini is 16,719 bp long and contains 13 mitochondrial protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and a putative control region between tRNA-P and tRNA-F distinguished by a single short noncoding region. Phylogenetic analysis using PCGs confirmed that this mtDNA sequence belongs to the family Pleuronectidae. This is the first study reporting the complete mitochondrial genome sequence of P. herzensteini.