We report the recovery and characterization of the complete mitochondrial genome of commercially and ecologically important giant clam, Hippopus hippopus. The total length of H. hippopus mitogenome was 22,463 bps (bp), comprising13 protein-coding genes, 23 tRNA genes, 2 rRNA genes and a non-coding control region. The control region was 3508 bp long and located between the trnM-atg and COX2 genes. We found the atp8 gene between trnF-ttc and NAD4 in the mitogenome of H. hippopus, which was absent in another giant clam species, Tridacna squamosa, as well as other bivalve species. Our new and first data of the complete H. hippopus mitogenome will offer genetic information that will be useful for furthering conservation genetics research of this threatened species.