We used a simulation model to examine the effect of area closures and fishing effort on the two main target species of the Great Barrier Reef Coral Reef Finfish Fishery: common coral trout (Plectropomus leopardus) and red throat emperor (Lethrinus miniatus). Area closures had greater effect on the more sedentary coral trout, in the areas outside the closures and accessible to the fishery, and little effect on red throat emperor, which was assumed to move among reefs. The effects of effort levels were greater than area closures on the harvest of both species and were seen not only in the areas accessible to the fishery, but also in the biomass of red throat emperor in the areas closed to the fishery. The catch and biomass resulting from a given effort level did not appear to have an equivalent effect attributable to any area closure. Although the effects of effort levels and area closures are confounded in reality by the coincidental implementation of area closures and restructuring of the fishery, the simulation model separated these factors to show that the closures under the 2004 rezoning should have had minimal effect on total-stock biomass and that a greater effect would result from changes in fishing effort.