Illegal, unreported and unregulated (IUU) fishing can lead to irreversible ecosystem changes; however, it is also one of the most difficult forms of fishing to manage and deter. In northern Australia over the past decade there has been a large increase in small-scale IUU fishing. We suggest that this small-scale fishing has arisen because of long-term fisheries over-exploitation in South East Asia. This IUU fishing forms part of the expansion-and-displacement cycle that can rapidly reduce biomass and alter the trophic structure of local ecosystems. With increasing human populations in the region, the pressure to fish illegally is likely to increase. Regional responses are required to deter and monitor the illegal over-exploitation of fisheries resources, which is critical to secure ecosystem stability as climate change and other destructive human activities threaten food security.