The complete mitochondrial genome of Epinephelus quoyanus is first presented in this article. It is a circular DNA double strand of 16,797 bp in length, consisting of 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA (tRNA) genes and a control region. The gene order and transcriptional orientation of E. quoyanus was same with most vertebrates. Several short overlaps and intergenic spacers were found at different gene junctions. Unusually, the CO1 gene started with GTG codon and the ATP6 gene started with CTG codon. The tRNA-Ser2 (GCU) lost the DHU stem. Within the control region, the termination-associated sequence was found near the tRNA-Pro and the conserved sequence blocks (1-3) were identified near the tRNA-Phe.
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