A simple bioeconomic leader-follower model was constructed to simulate snapper (family Lutjanidae) and grouper (family Serranidae) fisheries in Raja Ampat, Indonesia, an area of significant coral and fish biodiversity. We developed a leader-follower game, wherein the Regency government as the leader chooses an enforcement model to discourage illegal fishing. Fishers are then given a choice to fish using legal gears, such as handlines, or to fish with illegal gears, e.g. dynamite (for snapper) or cyanide (for grouper). Given prices and costs of legal and illegal fishing, the status quo simulations with no Regency enforcement result in a large amount of illegal catch throughout the 50 yr simulation, which agrees with expert opinion that destructive illegal fishing is occurring in the region. In an attempt to include ecosystem-based management principles into Raja Ampat governance, we introduce an enforcement regime in the form of detecting and punishing illegal fishing. Results suggest that current fishing practices do not account for the disproportionate ecosystem effects of destructive fishing, and that elimination of dynamite fishing may be easier for the government due to the high profitability of the live fish trade connected with cyanide fishing.