Dugong hunting by Torres Strait Islanders has a long history dating back at least 4000 years. Dugongs are highly susceptible to over-predation, due to slow development and low fecundity/reproductive rates. While attempts to model catch sustainability using recent survey and catch data have caused conservation concern, lack of historical data prevents reliable statements on the sustainability of past dugong hunting practices. In the absence of historical data, archaeological data in the form of dugong bones provide a unique and valuable data archive to examine long-term hunting sustainability in terms of changes in prey body size. Dimensional measurements of 229 ear bones (periotic bones) were used as a proxy for dugong size, to examine whether or not human hunting activity might have caused changes in dugong body size over time. Three archaeological sites of the Mabuyag Islands of the Goemulgal people of central western Torres Strait were selected for comparison–a village midden (Goemu) and two ceremonial dugong bone mounds (Dabangay Bone Mound and Moegi Sibuy), which span 1000 years up to c.1900 AD. Statistical analysis revealed periotic bone size from the three sites is remarkably similar. Despite their high susceptibility to over-hunting, our archaeological results do not provide evidence for over-predation of dugongs by the Goemulgal in the past.