In an eastern-Pacific coral assemblage at Devil’s Crown, Galápagos Islands, Ecuador, two coral species, Psammocora stellata and Cycloseris (Diaseris) distorta, form dense populations of unattached colonies on sand and rubble substrata. In the Galápagos, living C. (D.) distorta is found only at this single site, whereas populations of P. stellata are found throughout the Archipelago. Six cores dating to ~ 7700 yBP showed P. stellata to be dominant throughout the history of this isolated community, but C. (D.) distorta increased in abundance from ~ 2200 yBP and reached peak abundance between 1471 yBP and the present. The relative frequency of the two coral species may be linked to millennial-scale climatic variability, and this site may represent a refuge for C. (D.) distorta from unfavorable climatic fluctuations on millennial timescales. Our results demonstrate that some corals can persist in isolated populations for millennia.