A balanced trophic model of a Galápagos rocky reef system was constructed using Ecopath and Ecosim. The Ecopath approach allowed characterization of food web structure through integration of disparate ecosystem information derived from many years of study of Galápagos shallow-water rocky reefs. Ecosim and Ecospace routines enabled us to explore various hypotheses about system dynamics as well as potential solutions to conservation concerns about overfishing. A full series of functional group removal simulations resulted in estimations of interaction strengths and 'keystone' potentials for each of the 42 living functional groups in the model. Relative interaction strengths in a pristine unfished system are likely to be quite different from interaction strengths indicated by this present-day model. At present, humans extract food from very low trophic levels (mean trophic level=2.3) in Galápagos rocky reef systems because sea cucumbers and detritivorous mullets comprised 71 and 15%, respectively, of the total fisheries catch. Catch rates of sea cucumbers (Stichopus fuscus; referred to here as 'pepinos') are shown to be unsustainable, and the population should be declining rapidly. The exclusion of fishing from 23% of the total reef area, representing a hypothetical non-extractive zone, prevented the functional extinction of pepinos that our analysis predicted to occur with no areas protected (given 1999-2000 capture rates). Even with 23% of the hypothetical area protected, pepinos were predicted to decline overall to a stable 36% of their current estimated biomass. Pepino biomass was predicted to increase to eight times that of current levels if pepino fishing were stopped altogether.