Ecosystem-Based Fisheries Management (EBFM) represents a relatively recent concept and scientific paradigm-shift that has been internationally promoted to sustain healthy marine ecosystems and the fisheries that they support. Multiple tools have been designed for the analysis of the complexity of ecosystems and a diverse set of Ecosystem Models (EMs) have received special attention in the context of EBFM strategies. Nevertheless, because EBFM and EMs lack a universal strategy, there are obstacles to their implementation, mainly in developing countries. This is also the case in Mexico that has recently adopted EBFM to stop the deterioration of its fisheries resources. Because no single EM has as yet been identified to successfully contribute to all EBFM goals (societal participation, ecosystem dynamics, spatio-temporal variability, the balance between conservation and resource use, and integrated management), this thesis proposes a structured planning scheme, in which ecosystem modeling can effectively contribute to the decision-making process. In this planning scheme, the complementary use of EMs should be pursued according to the context of each specific area. Therefore, through a contextual factor analysis applied to the co-development of fisheries and environmental policies, six historical phases were identified in Mexico, in which there are infrequent, long periods of stability and frequent, short periods of radical change that alternate between stable and adverse situations. Because of this changing balance between contextual situations, the Mexican capacity building to support fisheries management is being updated, albeit gradually. In an attempt to design new ecosystem management methodologies while taking into account Mexico s context and EBFM goals, this thesis attempts to describe an ecosystem modeling method that uses a trans-disciplinary approach (Local and Traditional Ecological Knowledge, Pressure-State-Response framework, Loop Analysis, and Geographic Information System) to identify ecosystem-level management alternatives capable of diminishing fishing impacts. The viability of this trans-disciplinary approach was discussed using two Mexican fisheries areas: (1) the Upper Gulf of California (UGC), which is an area of official EBFM implementation where a Biosphere Reserve was established with the aim of preserving a high degree of biodiversity and remediating fishing impacts, and (2) the Huave Lagoon System (HLS), which is an area of communal management where two ethnic groups (Zapotec and Huave) have historically managed their fisheries resources using techniques rooted in a profound understanding of the ecosystem. In theoretical model simulations, the responses of both ecosystems to management strategies that allowed to protect top and mid trophic level species were analyzed. The trans-disciplinary approach explored by this thesis allow (1) to improve the fishermen s collaboration during the model-building process, (2) to increment the understanding of ecosystem effects of successful management strategies, (3) to understand the role of key interactions important in maintaining the services of the ecosystem, (4) to identify specific management strategies for each particular fishing seascape and temporal season, (5) to conceptualise the model in an environmental policy framework, analyzing the variables of the model as indicators of human activities and natural resources, and (6) to use of Local and Traditional Ecological Knowledge as information source
