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The complete mitochondrial genome of the coonstriped, Pandalus hypsinotus was determined by the MiSeq sequencing platform. The mitogenome of P. hypsinotus (15,909 bp) encoded the 13 protein-coding genes, 22 tRNA genes, two rRNA genes, non-coding, control region (D-Loop). Phylogenetic analysis based on the full mitochondrial genome sequences showed that P. hypsinotus is most closely related to P. borealis (86%) clustering together with Chlorotocus crassicornis in Pandalidae. The complete mitogenome sequence of P. hypsinotus would contribute to the scientific management for conservation of its resources in East/Japan Sea.