The El Niño Southern Oscillation (ENSO) drives important changes in the marine productivity of the Equatorial Pacific, in particular during major El Niño/La Niña transitions. Changes in environmental conditions associated with these climatic events also likely impact phytoplankton composition. In this work, the distribution of four major phytoplankton groups (nanoeucaryotes, Prochlorococcus, Synechococcus, and diatoms) was examined between 1996 and 2007 by applying the PHYSAT algorithm to the ocean color data archive from the Ocean Color and Temperature Sensor (OCTS) and Sea-viewing Wide Field-of-view Sensor (SeaWiFS). Coincident with the decrease in chlorophyll concentrations, a large-scale shift in the phytoplankton composition of the Equatorial Pacific, that was characterized by a decrease in Synechococcus and an increase in nanoeucaryote dominance, was observed during the early stages of both the strong El Niño of 1997 and the moderate El Niño of 2006. A significant increase in diatoms dominance was observed in the Equatorial Pacific during the 1998 La Niña and was associated with elevated marine productivity. An analysis of the environmental variables using a coupled physical-biogeochemical model (NEMO-PISCES) suggests that the Synechococcus dominance decrease during the two El Niño events was associated with an abrupt decline in nutrient availability (−0.9 to −2.5 μM NO3 month−1). Alternatively, increased nutrient availability (3 μM NO3 month−1) during the 1998 La Niña resulted in Equatorial Pacific dominance diatom increase. Despite these phytoplankton community shifts, the mean composition is restored after a few months, which suggests resilience in community structure.