Apostichopus japonicus (Selenka, 1867), is one of the economically important species cultivated in the adjacent seas in East Asian countries. Due to this importance, 17 complete mitochondrial genomes of A. japonicus are available now. Nucleotide diversity of 17 A. japonicus mitochondrial genomes exhibited gene-specific features, which can be utilized to develop mitochondrial molecular marker sequences for this species. Together with 191 A. japonicus mitochondrial sequences, nucleotide diversities calculated from only mitochondrial genomes and all available sequences present different patterns, which may reflect the different coverage of samples. These investigations of nucleotide diversity can be applied for understanding intraspecific characteristics of mitochondrial genomes of certain species in near future