Indonesia aspires to develop and implement policies for improved food security and economic prosperity through encouraging sustainable development of its aquatic living resources. However, Indonesia's knowledge sector lacks technical capacity to realise current policy aspirations. Its Universities can contribute to needed research and development but their engagement with government (central and regional) is underdeveloped. Accordingly, sustainable development of aquaculture and fisheries (prioritised by President Widodo and Fisheries Minister Ibu Susi) is impeded by knowledge gaps in aquaculture, fisheries science, fisheries management, supply chain management, business development and related issues such as aquatic animal health. Successful community-based management provides a pathway to developing sustainable enterprises from typically artisanal or subsistence operations. Australia can assist through capacity building and institutional strengthening to link the knowledge sector to the wider community through education and research. There are immense opportunities to transform Indonesia's knowledge sector, labour, and natural assets in strategic development of enterprises based on aquatic living resources across the archipelago. The proposed program engages the knowledge sector including prominent Universities to begin the needed capacity building and institutional strengthening process responsive to the government's current policy priorities.