Coral mortality caused by El Niño–Southern Oscillation (ENSO) activity and its related disturbances has been researched throughout the Eastern Pacific. In the past three decades, disturbances related to the El Niño–Southern Oscillation (ENSO) have been shown to influence coral growth in the Eastern Pacific. In the Galápagos Islands, Ecuador, more than 97% of corals experienced mortality after the severe 1982-1983 ENSO episode. However, two of the most dominant coral species found in a coral community adjacent to Devil’s Crown; Psammocora stellata and Diaseris distorta survived this severe ENSO event. By reconstructing sediment cores of the coral community, this study assessed how the coral assemblage has changed over the past 7,700 years of the Holocene epoch. The historical reconstructions were then related to existing records of Holocene ENSO variability in order to determine if changes in the relative abundance of coral species were related to ENSO activity and disturbances. We observed high variability in the relative abundances of P. stellata and D. distorta in the cores, including an increase in the abundance of D. distorta at approximately 2,200 yBP. Between the two species, opposite abundance trends were observed and supported by Detrended Correspondence Analysis (DCA) and Non-metric Multidimensional Scaling (NMDS) ordination analysis. Overall, the high variance in coral composition at the site throughout the Holocene documents repeated disturbance events in this region.