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The complete mitochondrial genome (16,497 bp) of the humpback grouper Cromileptes altivelis is first presented in this study. The gene arrangement and translate orientation of C. altivelis is identical to most vertebrates, including 13 protein-coding genes, 2 ribosomal RNA genes, 22 transfer RNA genes and a putative control region. The overall nucleotide composition of the H-strand is 29.80% A, 26.23% T, 15.67% G and 29.02% C. The origin of the light-strand replication was identified between the tRNA-Asn and tRNA-Cys genes, while the termination associated sequence (TAS) and conserved sequence blocks (CSB1-3) were identified in the control region.