Pollen and charcoal records from two large, shallow lakes reveal that throughout most of the past 50,000 yr Noel Kempff Mercado National Park, in northeastern lowland Bolivia (southwestern Amazon Basin), was predominantly covered by savannas and seasonally dry semideciduous forests. Lowered atmospheric CO2 concentrations, in combination with a longer dry season, caused expansion of dry forests and savannas during the last glacial period, especially at the last glacial maximum. These ecosystems persisted until the mid-Holocene, although they underwent significant species reassortment. Forest communities containing a mixture of evergreen and semideciduous species began to expand between 6000 and 3000 14C yr B.P. Humid evergreen rain forests expanded to cover most of the area within the past 2000 14C yr B.P. coincident with a reduction in fire frequencies. Comparisons between modern pollen spectra and vegetation reveal that the Moraceae-dominated rain forest pollen spectra likely have a regional source area at least 2–3 km beyond the lake shore, whereas the grass- and sedge-dominated savanna pollen spectra likely have a predominantly local source area. The Holocene vegetation changes are consistent with independent paleoprecipitation records from the Bolivian Altiplano and paleovegetation records from other parts of southwestern Amazonia. The progressive expansion in rain forests through the Holocene can be largely attributed to enhanced convective activity over Amazonia, due to greater seasonality of insolation in the Southern Hemisphere tropics driven by the precession cycle according to the Milankovitch Astronomical Theory.