The conservation and management of migratory species is complex and challenging. International agreements such as CITES and CMS provide frameworks to manage highly migratory species, but management can be compromised by lack of data and tractable mechanisms to integrate disparate datasets. Hammerhead sharks (Sphyrna spp.) are highly migratory species taken in coastal and oceanic fisheries around the world and are listed in CITES and CMS. A large scale assessment of scalloped hammerhead (S. lewini) and great hammerhead (S. mokarran) populations across northern Australia, Indonesia and Papua New Guinea was conducted to inform management responses to CITES and CMS. A simple Integrative Assessment Framework (IAF) was devised to systematically incorporate disparate data types across jurisdictions and create a regional synopsis. The IAF amalgamated data from fisheries catch records, fishery independent research, shark control programs, market surveys, BRUVS and citizen science data. Hammerhead populations are segregated by sex and size across the assessment area, with Australian populations dominated by juveniles and small sized adult males, while Indonesian and Papua New Guinean populations contained large adult females. The final IAF assessment stage introduced genetic and tagging data to produce conceptual models of regional hammerhead movement and stock structure. Several viable hypotheses for regional stock structure and movement patterns were produced, but more data are needed to identify the most plausible hypothesis. This work demonstrates a simple conceptual framework for assessing migratory species, and highlights priority areas for management and research of hammerheads in the Australasian region.