El Niño events heavily influence physical characteristics in the Tropical Eastern Pacific and lead to a decrease in nutrient and phytoplankton concentrations and to variation in the composition of the marine trophic chain. However, El Niño events can also provide an opportunity to evaluate the possible effects climate change may have on marine ecosystems. The Galapagos Marine Reserve coastal fin-fish fishery supports approximately 400 fishers that target species that include benthic/demersal predatory fish such as the endemic Galapagos whitespotted sandbass (Paralabrax albomaculatus), the regional endemic sailfin grouper (Mycteroperca olfax) and mottled scorpion fish (Pontinus clemensi), and the misty grouper (Hyporthodon mystacinus). The first two species are listed as vulnerable and endangered, respectively, on the IUCN red list of threatened species. Despite their potential effects on the biota, at present it is unclear how El Niño events influence artisanal fin-fish fisheries in the Galapagos. To study the impacts of El Niño events on the fishery, numerical percentage catch composition at the largest dock in Santa Cruz Island was recorded during March and April 2013, 2014 and 2016 and compared. Compositions were significantly different between 2016 and both 2013 and 2014, but not between 2013 and 2014. These differences appear to have been due to the appearance of uncommon demersal/benthic predatory fish such as Grape eye seabass (Hemilutjanus macrophthalmos) and Pacific dog snapper (Lutjanus novemfasciatus). Size frequency distributions also varied, with significantly larger sizes of several species observed in 2016 when compared to 2013 or 2014. These changes in catch composition and size may be a product of a reduction in nutrient concentration and primary production that led to an increase in water clarity and decrease in prey biomass that forced these benthic fish species to change their feeding behavior and strike at baits that usually would not be easily detected. Because of the conservative life history many of these benthic predatory fish exhibit and the absence of any form of management for fish species in the GMR, El Niño events may have profound effects on their populations due to the elimination of the largest individuals. Management actions, such as size and catch limits and closures, directed at reducing the impact of the fishery on these important fish populations in the near- (El Niños) and long-term (climate change) future should be encouraged.