The globally significant dugong population of Torres Strait supports an important indigenous fishery for meat and oil. The fishery is protected by the Torres Strait Treaty between Australia and Papua New Guinea. A time series of aerial survey estimates from 1987–2001 confirms that there is considerable temporal variability in the size of the dugong population in the region and adds to a growing body of evidence from other aerial surveys and satellite tracking that dugongs undertake large-scale movements associated with temporal and spatial changes in the distribution of their seagrass food. The magnitude of these effects on both the size of the population and the catch cannot be disaggregated from the effects of population depletion from over-harvesting. The Potential Biological Removal method was used in conjunction with the aerial survey data to estimate sustainable anthropogenic mortality from all causes for a range of empirically-derived estimates of dugong life-history parameters. These estimates of a sustainable harvest are so far below the current harvest that it must be unsustainable. Governments should heed the Islanders' requests for assistance in implementing co-management of the fishery as a matter of urgency.