A new paleolimnological dataset from Lake Pacucha (13 °S, 3095 m elevation) in the Peruvian Andes provides evidence of changes in lake level over the past 24,700 yr. A late-glacial highstand in lake level gave way to an early-Holocene lowstand. This transition appears to have paralleled precessional changes that would have reduced insolation during the wet-season. The occurrence of benthic/salt-tolerant diatoms and CaCO₃deposition suggest that the lake had lost much of its volume by c. 10,000 cal yr BP. Pronounced Holocene oscillations in lake level included a second phase of low lake level and heightened volatility lasting from c. 8300 to 5000 cal yr BP. While a polymictic lake formed at c. 5000 cal yr BP. These relatively wet conditions were interrupted by a series of drier events, the most pronounced of which occurred at c. 750 cal yr BP. Paleolimnological changes in the Holocene were more rapid than those of either the last glacial maximum or the deglacial period.

Controversy exists over the cause and timing of the extinction of the Pleistocene megafauna. In the tropical Andes, deglaciation and associated rapid climate change began ~8,000 years before human arrival, providing an opportunity to separate the effects of climate change from human hunting on megafaunal extinction. We present a paleoecological record spanning the last 25,000 years from Lake Pacucha, Peru (3,100 m elevation). Fossil pollen, charcoal, diatoms, and the dung fungus Sporormiella, chronicle a two‐stage megaherbivore population collapse. Sporormiella abundance, the proxy for megafaunal presence, fell sharply at ~21,000 years ago, but rebounded prior to a permanent decline between ~16,800 and 15,800 years ago. This two‐stage decline in megaherbivores resulted in a functional extinction by ~15,800 years ago, 3,000 years earlier than known human occupation of the high Andes. Declining megaherbivore populations coincided with warm, wet intervals. Climatic instability and megafaunal population collapse triggered an ecological cascade that resulted in novel floral assemblages, and increases in woody species, fire frequency, and plant species that were sensitive to trampling. Our data revealed that Andean megafaunal populations collapsed due to positive feedbacks between habitat quality and climate change rather than human activity.