Understanding the response of the El Niño-Southern Oscillation (ENSO) to global warming requires quantitative data on ENSO under different climate regimes. Here, we present a reconstruction of ENSO in the eastern tropical Pacific spanning the past 10,000 years derived from oxygen isotopes in fossil mollusk shells from Peru. We found that ENSO variance was close to the modern level in the early Holocene and severely damped ~4000 to 5000 years ago. In addition, ENSO variability was skewed toward cold events along coastal Peru 6700 to 7500 years ago owing to a shift of warm anomalies toward the Central Pacific. The modern ENSO regime was established ~3000 to 4500 years ago. We conclude that ENSO was sensitive to changes in climate boundary conditions during the Holocene, including but not limited to insolation. Copyright © 2014, American Association for the Advancement of Science.