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Ctenochaetus flavicauda is one of most important genera of Acanthuridae. However, the systemically classification and taxonomic studies have so far been limited. In this study, we report the complete mitochondrial genome sequence of C. flavicauda. The mitogenome has 15,772 base pairs (55.5% A + T content) and made up of total of 37 genes (13 protein-coding, 22 transfer RNAs and 2 ribosomal RNAs), and a putative control region. This study will provide useful genetic information for future phylogenetic and taxonomic classification of Acanthuridae.