Small-scale fisheries in the Galapagos Marine Reserve face significant challenges due to climatic anomalies and human-induced changes such as weak governance and overfishing. This overview explores the social-ecological impacts of the El Niño-Southern Oscillation (ENSO) and climate change on Galapagos small-scale fisheries, including the progress and challenges of ENSO and climate change research in this multiple-use marine protected area. The extreme El Niño events of 1982/83, 1997/98, and 2015/16 caused significant ecological shifts and fluctuations in fisheries productivity. While some species have shown increases in biomass, likely linked to sea surface temperature changes and altered ecosystem dynamics, the impacts on others remain uncertain or underexplored. Sailfin grouper (Mycteroperca olfax) and spiny lobster (Panulirus penicillatus and P. gracilis) fisheries have exhibited mixed responses to the El Niño, illustrating the complex nature of ENSO's ecological effects, which are further exacerbated by overfishing. The socio-economic impacts on fishing communities include reduced landings, longer search times, higher fishing costs, and increased livelihood insecurity. Future projections suggest an increasing vulnerability to ENSO and climate change, emphasizing the need for an ecosystem approach to fisheries. Key strategies include enhancing adaptive capacity, promoting sustainable practices, and adopting a social-ecological and transdisciplinary research approach. However, progress in ENSO and climate change research is hampered by weak governance, characterized by institutional barriers that hinder the formulation and enforcement of solid fisheries governance policies. To strengthen the resilience of Galapagos small-scale fisheries, interinstitutional and intersectoral collaboration is essential, supported by international cooperation and strategic investments to bolster local research capabilities.