Resumen: The structure and functioning of the food web of the Francisco Coloane Marine Area in the Magellan Strait, Chile, was quantified, with an emphasis on identifying the ecological role of the squat lobster (Munida gregaria) and the Fuegian sprat (Sprattus fuegensis). Food web indicators, the trophic level, and centrality indices were estimated using Ecopath with Ecosim. Dynamic simulations were carried out to evaluate the ecosystem impacts of biomass changes in squat lobster and Fuegian sprat. The model calculated a total ecosystem biomass of 71.7 t km−2 and a total primary production of 2450.9 t km−2 year−1. Squat lobster and Fuegian sprat were located in specific trophic levels of 2.3 and 2.7, respectively. Squat lobster reduction produced a decrease in the biomass of red cod (42–56%) and humpback whales (25–28%) and Fuegian sprat reduction a decrease in penguins (15–37%) and seabirds (11–34%). The Francisco Coloane Area is an immature ecosystem with productivity and energy flows values within those reported for productive ecosystems; the role of the squat lobster seems to be related to the structure of the food web, and the role of the Fuegian sprat seems to be related to the functioning of the ecosystem and to the energy transfer to top predators.