A high-resolution (2-9 year sampling interval) fossil pollen record from the Galapagos Islands, which spans the last 2690 years, reveals considerable ecosystem stability. Vegetation changes associated with independently derived histories of El Niño Southern Oscillation variability provided evidence of shifts in the relative abundance of individual species rather than immigration or extinction. Droughts associated with the Medieval Climate Anomaly induced rapid ecological change that was followed by a reversion to the previous state. The paleoecological data suggested nonneutral responses to climatic forcing in this ecosystem prior to the period of human influence. Human impacts on the islands are evident in the record. A marked decline in long-term codominants of the pollen record, Alternanthera and Acalypha, produced a flora without modern analogue before 1930. Intensified animal husbandry after ca. 1930 may have induced the local extinction of Acalypha and Alternanthera. Reductions in populations of grazing animals in the 1970s and 1980s did not result in the return of the native flora, but in invasions by exotic species. After ca. 1970 the trajectory of habitat change accelerated, continuously moving the ecosystem away from the observed range of variability in the previous 2690 years toward a novel ecosystem. The last 40 years of the record also suggest unprecedented transport of lowland pollen to the uplands, consistent with intensified convection and warmer wet seasons.