To study the intraspecific variation of the sea cucumber, Apostichopus japonicus, we sequenced three complete mitochondrial genomes, especially from different body color variants (green, black, and red) of Apostichopus japonicus in Geomum-do, Republic of Korea. The full lengths of green, black, and red sea cucumber mitochondrial genomes are 16,106 bp, 16,096 bp, and 16,107 bp, respectively. They all contain 37 genes (13 protein-coding genes, 2 rRNAs, and 22 tRNAs), and have an average 38.0\% of GC ratio. Two hundred thirty eight single nucleotide polymorphisms and 26 insertion and deletions were identified among three sea cucumber mitochondrial genomes. The phylogenetic analysis of A. japonicus with additional 14 available A. japonicus and two Parastichopus mitochondrial genomes were used as outgroups shows somewhat distinct three clades with body color patterns. Furthermore, there is no clear phylogenetic separation among Korean, Chinese, and Japanese individuals. These data will provide new insights and to facilitate the rapid growth of the sea cucumber aquaculture industry and its breeding programs.