The Gulf of Mexico Fishery Management Council (Council) manages deepwater corals in effort to conserve the habitat and ecosystem functions that provide refuge to economically important fisheries. In the Gulf, the distribution, species composition, and ecosystem services provided by deepwater corals remains poorly understood. In 2013, the Council hosted a workshop to identify areas supporting deepwater corals that may warrant additional conservation and management measures. However, there is concern that additional management measures may create user conflicts and it is vital to prioritize areas in need of management while minimizing disruptions to fishing activities. We developed a decision support tool using MARXAN that allows examination of various options to achieve conservation goals while minimizing costs (economic or other) as part of a management strategy evaluation. The MARXAN model considers both ecological and human use variables as inputs and can be used to facilitate policy making. For example, the Council is considering designating additional areas as habitat areas of particular concern with some areas limiting the type of fishing gear to protect deepwater corals.