The Galapagos Marine Reserve is one of the largest marine protected areas in the world, hosting a high species diversity and endemism and supporting economically important artisanal fisheries for local people and tourists. To ensure proper management and conservation of species in an ecosystem is necessary to determine the species’ contributions to ecosystem functions and organization. We characterized the structure and functioning of the southeastern Galapagos Archipelago shelf ecosystem by building a mass balanced Ecopath model representing the period 2001–2004. The model considered 72 functional groups, emphasizing endemic or threatened species (EoTS), commercial species and seven fishing fleets. Various ecological network analysis indicators were used to determine the status of the ecosystem. Structural and flow-based indices, trophic interactions among groups and keystone species indices were used to determine the ecological role of the species, while fishing pressure indicators were analyzed to determine the sustainability of the fisheries. The results indicate the ecosystem has a middle developing level, is stable and resilient. Marine mammals, sharks, birds and fish with high trophic level (TLs) play roles in maintaining the order of the ecosystem and its resilience. Among these groups highlight several EoTS (e.g., the Galapagos sea lion), and some species of commercial value (e.g., the Galapagos sailfin grouper). EoTS and commercial species are important contributors to the ecosystem structure, but those with a lower TL contribute the most to the energy transfer. These findings suggest that certain commercial species deserve more protection as they contribute in a similar way as EoTS to important ecosystem functions. Contrary to what was expected, the results suggest the fishing activities produce moderate impacts, mainly on fisheries target species, but without significantly affecting the ecosystem functions. However, further studies are recommended to reinforce these findings. This model provides information useful for the design of management strategies that balance the conservation and exploitation of the Galapagos marine resources.