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One complete mitochondrial genome (mitogenomes) was determined for Melanochlamys sp. (Cephalaspidae: Aglajidae). The mitochondrial genome size was 13,795 bp. The sequence contains two ribosomal RNA genes (rrnL and rrnS), 20 tRNA genes, and 12 protein-coding genes (PCGs). The A + T content of the complete mitochondrial genome sequence was 68.2%. The base composition showed a tendency of high AT. The resulted maximum-likelihood (ML) tree of Opisthobranchia supported that genetic differences between Melanochlamys sp. with other species of Cephalaspidae, so that there is a well-defined separation of clades.