The neotropical Amazonian and Andean plant diversity developed mainly during the Tertiary. In Amazonia, Miocene floral diversity seems considerably higher than today. During the Neogene, tropical taxa entered newly created montane area, and montane taxa entered the tropical lowlands. The general decrease of temperature during the upper Neogene and especially during the Quaternary glacial periods may have caused considerable extinctions in the lowlands. Representation of pollen of apparently principally montane taxa ( Podocarpus, Hedyosmum) in Miocene, Pliocene, and Quaternary sediments of Amazonia and surroundings, is still difficult to interpret in terms of temperature decrease at low elevation. Changes in precipitation may have profound impact on the composition of vegetation communities; Ilex and Melastomataceae increase significantly in many glacial pollen records. Increase of Weinmannia in Amazonian pollen records seems the best indicator of downward migration of montane vegetation belts. A temperature lowering at sea-level of 4.5 ±1°C during the Last Glacial Maximum (LGM) seems reasonable; it may have caused a downslope migration of some 700 m of the lower montane vegetation belt; lower montane arboreal species may have been able to grow in higher elevation areas (>500 m) of Amazonia, increasing background pollen values of montane taxa in the area. Difference between a cool and wet Middle Pleniglacial (60-28 ka BP), and a cold and dry Upper Pleniglacial (28-14 ka BP; thus including the LGM) is evident in Andean and Amazonian records; statements about environmental conditions of the ice-age Amazon should be specified chronologically. The Middle Pleniglacial is a time of accumulation of fluvial sediments. The Upper Pleniglacial is a time of incision of the rivers in their sediments; sedimentation started again in the Lateglacial (since ca. 13 ka BP) and the Holocene, when lake levels rose again. Based on simplified considerations of precipitation changes and evaporation we estimate that LGM rainfall may have been reduced by values of ca. 45(±10%); Amazonian and Cordilleran lakes dried up; dry rain forest was locally replaced by savanna, savanna forest, or cerrado-type vegetation; dry rain forest, savanna forest, and pure savanna was locally replaced by extensive semi-desert dune formations (lower Rio Branco area in present-day central Amazonia). The present-day centers of higher rainfall (>2500 mm) surrounded by areas of lower rainfall, are refuge areas of the very wet rain forest and of the very high plant diversity (300 plant species per 0.1 ha), and they should have been that equally, or more, during the dry climate intervals (plant diversity of drier forests is in the order of 100-150 species per 0.1 ha). Both extinction and speciation in isolation under precipitation and temperature stress may have taken place in these refugia.