In this study, the complete mitogenome sequence of the palette surgeonfish, Paracanthurus hepatus (Perciformes: Acanthuridae), has been sequenced by next-generation sequencing method. The assembled mitogenome was 16 498 bp in length, consisted of 13 protein-coding genes, 22 transfer RNAs, 2 ribosomal RNAs genes. The overall base composition of palette surgeonfish was 28.6% for A, 28.6% for C, 16.3% for G, 26.4% for T and showed 87% identities to somber surgeonfish Zebrasoma flavescens. The complete mitogenome of the palette surgeonfish provides essential and important DNA molecular data for further phylogeography and evolutionary analysis for surgeonfish's phylogeny.