Indonesia is one of the largest exporters of groupers, both live and dead, as part of the reef fish food trade. These fisheries sub-sector plays an important role in the livelihoods of fishing communities, especially for those living on small islands. The aim of this article is to provide a baseline profile of the trade as currently practiced and develop a framework strategy for establishing a sustainable grouper export trade for Indonesia. Challenges faced in managing the country’s (both live and dead) grouper fishery and trade include the overfishing of groupers, catch of sexually immature groupers, exploitation of grouper spawning aggregation, illegal and unreported fishing for live groupers and overall lack of management or monitoring of grouper fisheries. These factors, collectively, have resulted in declining wild grouper stocks. Management and export trade of these fisheries requires regular and standardized monitoring, management and trade controls. Control on minimum size, fishing quotas and improved spawning aggregation protection to ensure sustainability are needed in addition to oversight of vessel activity to control the trade, especially exports. To maintain viable stocks, it is essential to safeguard adequate spawning capacity and reduce the illegal fishing methods (particularly potassium cyanide and compressor diving). In particular, it is important to ensure that sufficient fish become sexually mature and that sufficient adults are able to breed, particularly those that depend on aggregating to spawn because they are easy to over-fish in such time, requiring their seasonal and/or spatial protection from fishing. Since the grouper fisheries are particularly heavily driven by export markets, regulating volumes and sizes exported, especially oversight of at-sea and air cargo exports is needed. Immediate measures are essential to stop further declines and begin to rebuild grouper stocks in Indonesia.