Currently plants in the lowland Amazon are threatened primarily by local deforestation and land-use change. The Amazon rainforests contain an enormous amount of plant diversity, yet much of this diversity is located within very small ranges. As such, many plant species only exist in a small geographic area, and can be exterminated with small-scale deforestation events.

While lowland vascular plant species in the tropical rainforest are mostly threatened by deforestation, plants in the Amazonian cloud forests may be threatened by shifts in climate. As the climate warms, plants living on mountainous slopes will need to migrate higher in elevation to find a suitable climate in which to survive. If climate changes occur at rates faster than species can migrate, local extinction is a possibility. Only through migratory corridors created specifically for species to migrate effectively will many species survive the combined threat of land-use change and a warmer and drier climate in the Amazon.