Here we describe the complete mitochondrial genome sequence of humphead parrotfish, Bolbometopon muricatum. The circle genome (16,788 bp) consists of 13 protein coding, 22 tRNA, 2 rRNA genes and 1 control region. Generally it has the typical vertebrate mitochondrial gene arrangement but for the relative positions of the tRNAIle, tRNAGln, and tRNAMet, and a tRNAMet psuedogene was detected. This work provides fundamental molecular data which will be useful for species identification, forensic genetics and further researches on genetic diversity and conservation of this vulnerable marine fish.