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The mitochondrial genomes of Seriola quinqueradiata and S. lalandi were 16,539 and 16,535 base pairs long, respectively, whose organizations were similar to those of other bony fishes. The sequence similarity of two species was 93% in the mitochondrial whole genome. Between each coding gene, rRNA, and control region, the highest similarity was 98% in ATP8 and lowest similarity was 87% in the control region. Phylogenetic analysis of Carangidae mt 12 protein-coding genes showed that Seriola and Carangoides do not form a monophyletic genus.