Abstract Sustainable blue economies have become a priority policy for coastal and island countries. It is also the case for Indonesia as it is an archipelago country endowed with a wide-spreading ocean. It must be sustained by key guiding policy principles such as environmental conservation, sustainable management of natural resources, and livelihood improvement. These policy objectives must be pursued in an integrated and coherent manner. Yet, Indonesia faces multiple governance challenges to achieve such goals. Multi-stakeholder and cross-sectoral collaborations are indispensable. Innovation is also needed for policy development, technological advancement, and social partnership. Capacity development is a policy imperative at the local, sub-national, and national levels. International partnership is also important to promote transboundary and sub-regional ecosystem-based and collective marine resource management in the context of achieving sustainable blue economies particularly, through sustainable fisheries and eliminating illegal, unreported, and unregulated fishing. Multifaceted and interdisciplinary approaches need to be reinforced to overcome composite challenges.