The southern portion of South America, which encompasses high and exceptional lineage diversity, is well-suited to studies addressing the interaction between biogeography and local environmental conditions and how this historical process and environmental variables affect distribution patterns. We here assessed the role of environmental variables and spatially autocorrelated processes in driving tree species distribution patterns in the whole southern South America forests. We compiled a dataset containing 110,087 occurrence records of 3183 species distributed into 742 sites across six countries and 13 biomes. We modeled the influence of both environmental and spatial variables related to geographic distribution limitations on the variations of species composition through partial canonical redundancy analysis. We built such models for each of our four datasets: the whole extratropical area of South America; Atlantic and Pampa Biomes; dry communities east of the Andes; and communities west of the Andes. Both spatial and environmental variables affect tree species composition in the southern region of South America, although a major role is played by the “pure” spatial fraction. This greatest significance of spatial structures reinforces the importance of historical process for this region and the floristic dissociation existing between the tropical and extratropical portion of South America. We argue that the southern South American forests (especially their temperate portion) should not be lumped into the Neotropical Floristic Province, an idea of utmost importance for the conservation of these high-diversity austral forests.