This dissertation will be focused in the development and calibration of an integrated bioeconomic model of the nearshore Galapagos fishing sector. This model will analyze the complex interactions between policy options, the economic incentives they generate, the decisions motivated by those economic incentives, and the effects of those decisions on the biological health of the marine resources of the Galapagos Marine Reserve (GMR). First, the model will structure what is known about the marine systems of the GMR, and also will help identify those components which are less understood. Second, the model will help comprehend the consequences of uncertainty over the marine resources and the effects of that uncertainty over policy choices. Finally, the model will be used to to evaluate the effects of different management frameworks taking into account spatial considerations, including impacts of policies aimed at one fishery that have spillover effects on others. Hence the main goal of this research is to design a flexible instrument that permits to analyze both a range of policies and design options so that stakeholders of the Galapagos Marine Reserve (GMR) can contemplate a wider spectrum of possibilities and have a basis from which to engage in policy discussions.