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The sharp climatic contrast from east-west in subtropical and temperate South America is caused to a great extent by the Andean topography. This contrast determines a continuous and arid vegetational belt that crosses diagonally the continent from SE to NW, interrupting the region of the Chilean-Argentinean southern forests from other forests of South America, the so called ’Arid Diagonal of South America’. The purpose of this paper is to study the particular history of the process of isolation of the southern forests, using the phytogeographical and paleobotanical perspectives. The comparisons of the taxa richness, at different taxonomic levels, degrees of endermism, and geographical distribution ranges of species show the particular characteristics of the southern South American forests, which were interpreted as a syndrome of long-lasting geographical isolation. Thus, the great diversity of families represented in these forests (48.9% of the vascular flora of continental Chile) contrasts with the small number of species (7.8%); high frequency of taxonomically isolated genera (monotypics, 21%); and the high percentage of endemic seed plant species (90%), all suggests that the isolation of these forests and high rates of extinctions are of great geological antiquity. The phytogeographical analysts at a generic level shows that the endemic component of these forests is also very high (32%). The high proportion of neotropical (28%) and australasian (20%) elements is marked, pointing to floristical connections with distant territories, such as Australasia and tropical South America. The phytogeographical analysis based on the Chilean fossil record dating to the Tertiary shows that approximately 60% of the tropical genera present in Chilean paleo-forests disappeared at the end of the Paleogene. This resulted from a significant northern retreat of the tropical belt of the Southern Hemisphere, which was in turn a consequence of the separation between Australia and Antarctic continents, as well as subsequent changes in the oceanic and climatic systems associated with the formation of the East Antarctic ice cap. A number of remnant tropical genera still survive in the tropical Province of Yungas. A great proportion of the present endemic element of the Chilean-Argentinean forests is registered during the Neogene, but it was during the Miocene when similar floristic assemblages analogous to some of the actual types of subtropical and temperature forests rised, as is shown by the paleobotanical evidence. Also until the Miocene there was a geographical continuity of these forests: across subtropical South America, under mesic climatic conditions with little seasonality. This would explain the present floristic relationship between southern South American forests and those found in Planalto of southern Brazil and NW Argentina. During the Pliocene, the distribution of the subtropical forests of South America was fragmented and xeric formations expanded along the ’Arid Diagonal’ of the continent. These changes were a consequence of strong arid trends in the subtropics due to the final uplift of the Andes, the formation of the West Antarctic ice cap, intensification of the cold Humboldt Current and the South Pacific Subtropical Anticyclone, as well as the beginning of the continental glaciations in Patagonia. As the center of the ’Arid Diagonal occupied a nearly constant position during the glacial periods of the Quaternary, repeated advances of Andean glaciers and associated periglacial processes shaped the present distributional patterns of the southern Chilean-Argentinean forests.