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The complete mitochondrial genome of Otaria byronia was sequenced for the first time. The mitogenome is 16,640 bp long and encodes 13 protein-coding genes (PCGs), 22 tRNA genes, two rRNA genes, one origin of light strand replication (OL), and a control region (CR). The overall base composition is 33.1%, 27.0%, 14.2%, and 25.7% for A, C, G, and T, respectively. The CR with 1186 bp is in the position between tRNA-Phe and tRNA-Pro genes. Phylogenetic analyses show the classification status of the pinniped species and reveal that O. byronia is grouped to the Family Otariidae.