Ecosystem-based management is widely recognized as a fundamental approach to ensure marine life conservation. Understanding species roles is crucial, yet conservation efforts often prioritize charismatic or commercially valuable species rather than those functionally important. The Gulf of California’s food web, a ”world aquarium” of biodiversity, was analyzed to assess its resilience and structure using a topological approach across summer and winter seasons. Employing global and node-level properties and, secondary extinction simulations, the study evaluated 32 network configurations, including original seasonal networks and extinction scenarios for charismatic, commercial, and structurally relevant species. Results revealed significant seasonal structural shifts: summer networks were modular and compartmentalized, promoting local stability, while winter networks exhibited greater integration and connectivity, enhancing global robustness. Node-level analyses identified Lolliguncula spp. and the blue shrimp (Penaeus stylirostris) as critical species due to their roles in energy flow and ecosystem stability. Redundancy metrics underscored low bottom-up and top-down redundancies indicating structural vulnerabilities. Secondary extinction simulations highlighted the ecological and economic dual role of commercial species, particularly the blue shrimp, whose removal caused cascading species losses across the food web. These collapses occurred even when predators retained a large part of their diet, as we simulated different levels of dietary dependency in the absence of abundance data. This study identifies structural vulnerabilities and functionally significant nodes, offering actionable insights for conservation planning. Network analysis is essential to design sustainable and inclusive management strategies tailored to the unique ecological, economic, and cultural priorities of the Gulf of California.

Recognition of ecosystem-based management for marine life conservation is growing. Understanding key species roles is crucial, yet conservation efforts often prioritize charismatic or commercially valuable species. Here we quantified the topological importance of species with high economic or conservation value by simulating extinction scenarios in the Gulf of California trophic network. We found food web robustness against removals of charismatic or commercially important species while, others without such interests suggest strong roles on food web functioning. Invertebrates such as squids and crustaceans are in crucial intermediate positions, making them key bottlenecks for energy transfers. A mixed ecosystem control is at play in the food web, which is dominated by species controlling the indirect effects in top-down forcing as white sharks and hammerheads and bottom-up forcing imposed by the phytoplankton. Direct effect transmission is regulated by the silky shark due to its diverse diet. Only two charismatic removals, blue whale and white shark affected the closeness centrality patterns, whereas only blue shrimp and Monterrey sardine are commercially important species with functional relevance roles in the food web. In addition, our findings highlight the major structural importance of some non-charismatic species, as loliginid squid and blue shrimp populations, which in turn, impact indirectly on the charismatic species. We hope our network analysis will help decision makers in the development of novel conservation policies.