Context Currently, little information exists describing the population structure of great hammerhead sharks (Sphyrna mokarran) in Australian waters.

Aims This study used single nucleotide polymorphisms to investigate fine-scale population structure in S. mokarran across the Indo-Pacific.

Methods DNA was extracted from 235 individuals across six Australian locations and a Red Sea outgroup. Population parameters were calculated and visualised to test structuring across locations.

Key results No fine-scale population structuring was observed for S. mokarran across the Indo-Pacific. However, population structuring occurred for all Australian locations when compared to the Red Sea outgroup.

Conclusions Findings suggest a single stock is most likely for S. mokarran found in Australian waters. Results provide key information for understanding the broad range movements of S. mokarran and help to define the scale of management required to preserve genetic diversity in this species. The structuring between Australia and the Red Sea indicates limited gene flow and movement.

Implications Results indicate that large-scale movements of S. mokarran could be occurring to facilitate genetic mixing. Future research focusing on individual tagging to corroborate movements would be highly beneficial to determine how far (and often) individuals are dispersing, and to note where cross-jurisdictional management, including from neighbouring regions in the Indo-West Pacific–Oceania region, are most critical.