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The complete mitochondrial genome of the morotoge shrimp, Pandalopsis japonica was determined by the high-throughput sequencing technique. The mitogenome of P. japonica (15,909 bp) encoded the 13 protein-coding genes (PCGs), 22 tRNA genes, 2 rRNA genes as well as the non-coding control region (D-Loop). The mitochondrial genome of P. japonica showed an identical gene arrangement in its mitochondrial genome to its relative Pandalid shrimps including P. borealis and P. hypsinotus. Among 13 compared mitogenomes within order Suborder Pleocyemata, P. japonica was most closely related to P. hypsinotus with 86% sequence identity clustering together with three other shrimps in family Pandalidae.