Efforts to conserve marine biodiversity must move beyond conserving individual species within protected areas and seek to preserve the functional roles that species perform in ecosystems across seascapes. For instance, herbivorous and predatory (including invertebrate-feeding) fish are critical for maintaining coral-reef habitat and the diversity of dependent fish assemblages. However, increasing the biomasses of fished species may come at a cost to fisheries. Using coral reefs as an example, we examined critical functional roles and model trade-offs between fishery profits and the spatial extent of functional fish communities. The nature of the trade-off depended on the management scenario: protecting functions in small areas could be achieved with marine reserves at minimal cost to fisheries, whereas reducing fishing effort was a more effective method for protecting functional communities across a seascape. An appropriate choice of management actions can alter the trade-off and, in doing so, ameliorate potential for conflict with resource users.