The great hammerhead (Sphyrna mokarran) is considered a semi-solitary and highly migratory species, with a circum-global distribution. The species is listed as critically endangered on the IUCN Red List of Threatened Species, and global trade is restricted under the Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) and the Convention on Migratory Species (CMS). Despite this, commercial harvest and export for meat and fins across their range in Australia, Papua New Guinea and Indonesia still occurs. Within Australia, S. mokarran is listed as vulnerable and despite reports of overfishing and depletion, this allows for commercial fishing of the species within set regions operating under a strict total allowable commercial catch (TACC) limit. Currently little information exits for population structure of S. mokarran in Australian waters, despite an understanding of genetics being a major consideration to appropriate stock assessment modelling and subsequent fishery management arrangements. This research aims to identify the population structuring and connectivity of S. mokarran with a focus on Australian Exclusive Economic Zone (EEZ) waters. Population genetics has been an important tool in fishery management, previously revealing strong population differentiation for other species in the Sphyrnidae family (S. lewini and S. zygaena) with a multi-use approach of genetic markers (microsatellites and single nucleotide polymorphism (SNPs)). SNPs allow for fine-scale population structure detection among Australia’s TACC zones. Results from the study presented here will be subject to a more appropriate sample size, a factor insufficient in previous research, so adequate conclusions can be made on the structuring of S. mokarran within the Australian EEZ. Outcomes from such research will be useful in delineating S. mokarran populations in Australia to manage the commercial economic viability and their continued conservation in fisheries management.