La Parguera, Puerto Rico, a well-studied Caribbean reef system, is showing signs of overfishing and thus, is a good candidate to evaluate fishery policy scenarios using ecosystem modeling. The first steps taken to build a plausible ecosystem model of the La Parguera reef system using Ecopath with Ecosim software included synthesizing fisheries and ecological data then balancing and analyzing trophic relationships for the year 2000. The model is centered around species of commercial and ecological importance in the ecosystem, grouped by habitat preferences. Model construction identified gaps in available data (e.g., diet compositions, metrics of fishing effort, incomplete landings) and balancing raised interesting ecological questions. Some groups, such as parrotfish are so underutilized as prey that the accuracy of biomass estimates and our understanding of predator-prey relationships are questioned. Apparent shortcomings in estimates of primary production relative to consumer biomass generated questions of whether estimates are inaccurate or whether the system is highly subsidized by importation from outside ecosystem boundaries. Although details are not directly comparable because of different structures, a similar Carribean model built for the 1970–1980s estimated total biomass 5.6 times higher than the present model. Changes of this magnitude, if found to be accurate, point out the need for further study of the roles fishing and environmental change have played in reshaping this system over the last 30–40 years. This modeling effort defined future data needs, generated hypotheses for further coral reef research, and provided a starting point towards evaluation of fishery management scenarios in an ecosystem context.