We present the first mitochondrial genome sequence of the great hammerhead shark, Sphyrna mokarran. This species is of considerable conservation concern throughout its global distribution, and currently listed as Endangered on the IUCN Red List. The mitochondrial genome is 16,719 bp in length with 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes and a non-coding control region. The gene arrangement is congruent with other shark and most vertebrate species. This S. mokarran mitogenome provides a genomic resource for assisting with population studies and conservation efforts for this highly depleted species.