The complete mitochondrial genome of Calanus simillimus is 27,876 bp in length (GenBank accession OK500294) and containing 13 protein-coding genes (PCGs), 2 rRNA genes, 22 transfer RNA genes. The gene order is novel compared to other Calanus species and copepods with sequenced mitogenomes. Phylogenetic analysis suggests that C. simillimus represent a fourth group within Calanus genus in addition to C. hyperboreus, C. finmarchicus and C. helgolandicus groups. The complete mitochondrial genome of C. simillimus will be useful for species identification, population genetics, phylogenetic and evolutionary studies among copepods.