The first paleoecological analysis of a complete sedimentary record spanning the period from the late Pleistocene to the present from lowland Panama, documents changes in lowland vegetation communities through major climatic change and the onset of human disturbance. Past sympatry is found among presently allopatric species, suggesting that tropical forest communities are not species-stable through time. Late Pleistocene floras at Lake La Yeguada (elevation 650 m), Panama, had high relative abundance of montane forest elements, e.g., Quercus and Magnolia, existing some 900 m below their present range, suggesting a climatic cooling of almost-equal-to 5-degrees-C below present. This descent of montane forest taxa onto lowland hilltops denied the ground to postulated lowland rain forest refugia. The late Pleistocene (14350-11050 yr BP) was not uniformly cool and was interrupted by brief phases of near present-day warming. The onset of the Holocene was abrupt, taking < 100 yr, and was almost coincidental with the start of human forest disturbance. Changes in climate at La Yeguada were found to be largely synchronous with those documented at Lake Valencia, Venezuela, but no fine-scale climatic synchrony was apparent with South American or European sites, and significant departures from the predictions of published climatic circulation models are found.