In 2000, longline fishing was banned inside the Galapagos Marine Reserve to prevent illegal fishing of sharks and bycatch of endangered, threatened, and protected (ETP) species. Despite local management institutions possess one of the most sophisticated control and surveillance systems in the Eastern Tropical Central Pacific, statistical and anecdotic evidence suggest the longline ban has been ineffective in eradicating illegal, unreported and unregulated (IUU) fishing for the last two decades. This short communication examines the legal, institutional, and socio-economic factors that have prevented the effective implementation of the longline ban and proposes an ecosystem approach to fisheries to maintain bycatch mortality rates below biologically based limits, facilitating the recovery of ETP species while safeguarding a sustainable development of the Galapagos small-scale tuna fishery. Significant investments in science, technology, and innovation are necessary to encourage gradual and adaptive improvements in fishing practices to reduce IUU fishing and bycatch.