Oceanic phytoplankton respond rapidly to a complex spectrum of climate-driven perturbations, confounding attempts to isolate the principal causes of observed changes. A dominant mode of variability in the Earth-climate system is that generated by the El Niño phenomenon. Marked variations are observed in the centroid of anomalous warming in the Equatorial Pacific under El Niño, associated with quite different alterations in environmental and biological properties. Here, using observational and reanalysis datasets, we differentiate the regional physical forcing mechanisms, and compile a global atlas of associated impacts on oceanic phytoplankton caused by two extreme types of El Niño. We find robust evidence that during Eastern Pacific (EP) and Central Pacific (CP) types of El Niño, impacts on phytoplankton can be felt everywhere, but tend to be greatest in the tropics and subtropics, encompassing up to 67% of the total affected areas, with the remaining 33% being areas located in high-latitudes. Our analysis also highlights considerable and sometimes opposing regional effects. During EP El Niño, we estimate decreases of −56 TgC/y in the tropical eastern Pacific Ocean, and −82 TgC/y in the western Indian Ocean, and increase of +13 TgC/y in eastern Indian Ocean, whereas during CP El Niño, we estimate decreases −68 TgC/y in the tropical western Pacific Ocean and −10 TgC/y in the central Atlantic Ocean. We advocate that analysis of the dominant mechanisms forcing the biophysical under El Niño variability may provide a useful guide to improve our understanding of projected changes in the marine ecosystem in a warming climate and support development of adaptation and mitigation plans.