Human communities, including the great empire of the Incas, have lived in the Tropical Andes for thousands of years. Because the Inter-Andean valleys are the most hospitable to people, they are also the most degraded parts of the hotspot, with less than 10 percent of their original habitat remaining. At the other end of the spectrum, some of the least degraded parts of the hotspot include isolated regions in Venezuela and Colombia, and the eastern slope of the Andes in Bolivia, Peru, and parts of Ecuador. In Peru and Bolivia particularly, time still exists to establish reserves in areas of intact primary forests. However, the effects of a large and growing population continue to threaten biodiversity in the Tropical Andes. Several cities with millions of inhabitants, including Santa Fe de Bogotá, Colombia; Quito, Ecuador; Arequipa, Peru; and La Paz/El Alto, Bolivia, are located within the hotspot and continue to expand as their populations grow. In total, it is thought that no more than about 25 percent of the original vegetation of this hotspot remains intact.
In the cloud forests, agriculture, deforestation, dams, and road building are the most significant threats. At higher altitudes, seasonal burning, grazing, agriculture, mining, and fuelwood collection have degraded the grasslands and scrublands of the puna and páramos. Extensive cultivation of opium poppy has led to the clearing of thousands of hectares of montane forests and the spread of chemical herbicides through rivers and streams that pose additional threats to plant and animal species, especially amphibians. Guerilla activities associated with this trade often make it difficult to sustain conservation activities in the area safely.
In the lower altitudes, a new and serious threat is oil exploration and development on the eastern slopes of the Andes and the adjacent Amazonian lowlands of Colombia, Ecuador, Peru, and Bolivia. In recent decades, large oil and gas discoveries have been made in these areas, making the region a hydrocarbon hotspot as well as a biodiversity hotspot. Industrial and small-scale mining for diamonds, iron ore, gold, and bauxite also pose threats throughout the hotspot. The growing network of roads that accompanies this industrial development is also bringing waves of migrants fleeing economic hardship in the highlands.
Finally, invasive alien species, many of which were introduced as human food sources or to facilitate agriculture, threaten the survival of native flora and fauna. Alien species include exotic grasses used for cattle grazing, the rainbow trout (Salmo gairdnerii), and the American bullfrog (Rana catesbeiana), which can out-compete or even eat many native amphibians.