During 2015–2016, a strong El Niño event, nicknamed the “Godzilla El Niño,” occurred in the Pacific Ocean. Using satellite imagery, in this article we assess impacts of this event on sea-surface temperature and chlorophyll-a concentrations in the southern Gulf of California. Daily images of sea-surface temperatures and chlorophyll-a were obtained by satellite from the Moderate Resolution Imaging Spectroradiometer for the period from January 2013 to December 2017. A circular area ≈ 46.8 km in diameter in the central part of the gulf was selected to evaluate monthly variation of both parameters. Hydrographic data generated during a research cruise in November 2016 were used to evaluate water mass distributions. Results revealed strong seasonal variability, with high chlorophyll-a concentrations recorded during winter and low values during summer. Contrary to predictions, the “Godzilla El Niño” event apparently did not have as large an impact on the phytoplankton biomass, expressed as chlorophyll-a, in this region in comparison to other areas and to previous strong El Niño events. This is likely related to gulf dynamics and to the mechanism of productivity enhancement, although further observations are required to confirm this theory. Results presented contribute to a better understanding of the highly productive and unique Gulf of California ecosystem.