We surveyed coral reefs communities before (September 2007–March 2009) and during (September 2009) the 2009–2010 El Niño event on the coast of Oaxaca, southern Mexican Pacific to evaluate community changes associated with the warming event. From May 2009 to December 2010, we recorded positive deviations from the historical in situ sea surface temperature values. There were differences among the coral species Pocillopora damicornis, Pavona gigantea, and Porites panamensis with significant reductions in chlorophyll a and Symbiodinium density during El Niño, resulting in bleaching (>13%) and increase in algal coverage (mainly geniculate coralline algae). Concurrently, echinoderm and fish assemblages also experienced significant modifications; abundances of the sea urchins Eucidaris thouarsii and Centrostephanus coronatus increased during the warming event, whereas Diadema mexicanum declined; meanwhile, fish species such as Thalassoma lucasanum declined in favor of Stegastes acapulcoensis and Haemulon maculicauda during the warming event. During the El Niño event, changes in composition and abundance of echinoderms and fish may have been due to horizontal and/or vertical redistribution of species rather than species mortality or recruitment. The observed changes in coral physiology and consequent modifications in coral, echinoderm, and fish communities highlight that the 2009–2010 El Niño event impacted several levels of biological organization in the coral reefs of southern Mexico, beyond the actual corals themselves. The observed changes add to local stressors associated with coastal development and ultimately threaten the health of the once considered best-developed reef system in the Eastern Pacific.