Fluctuations of Galapagos mid-water and benthic reef fish populations during the 2015–16 ENSO

El Niño Southern Oscillation (ENSO) events have impacted the marine environment of the Galapagos, causing massive die-offs of corals and megafauna, and benthic habitat shifts. With ENSO events predicted to intensify under climate change scenarios it is important for managers to have an evidence-based understanding of how these events may affect fish assemblages in the Galapagos. We assess the abundance and size fluctuations of benthic and mid-water shore fishes during the 2015–16 “Godzilla” ENSO using data from baited remote underwater stereo-video surveys collected on four occasions over 2015–16. We found significant differences in the assemblage structure between the pre-El Niño, El Niño onset, El Niño receding, and La Niña onset sampling periods. Mackerels (i.e. Trachurus murphyi and Decapterus spp.) had a ∼480% greater relative biomass, 229% greater relative abundance, and 20.6% greater size during La Niña onset compared to El Niño. With the onset of La Niña we observed a severalfold increase in the abundance of mid-water species including large Carangids, medium-size Scombrids, elasmobranchs (i.e. Sphyrna lewini, Carcharhinus galapagensis) and several other bentho-pelagic taxa. We also found evidence of seasonal abundance fluctuations across years, independent of seasonal effects, in Scarids, Haemulids, Labrids, Chaetodontids, and Carangids. Although the 2015–16 ENSO appears to have had a lesser impact on the Tropical Eastern Pacific than past El Niño events, it was linked to changes in the abundance of several species of key ecological and economic importance. This information furthers our understanding of the influence of large-scale climatic events on fish populations and improves our ability to predict how these populations may change under future climate scenarios. •Significant changes in Galapagos fish assemblage structure linked to 2015–16 ENSO.•Mackerels displayed marked fluctuations in size and abundance during ENSO.•Changes in other fish taxa including carangids, scombrids, and elasmobranchs.•ENSO impacts Galapagos fish species of key ecological and economic importance.•Important implications with projected ENSO intensification due to climate change.