The cloud forests of the Junin area of Ecuador are in the confluence of two of the world's hottest of biological hotspots; the Chocó-Darien Western Ecuadorian and the Tropical Andes. Although only a sixth of the largest hotspot, the Tropical Andes is considered the single richest hotspot on the planet. It contains approximately 15-17% of the world's plant species and nearly 20% of its bird diversity (1,666). Over 40% of the area's plant and bird species are endemic to the region.

Furthermore, a large portion of the Reserve is home to primary forests. Significant portions of these forests are cloud forests. According to the United Nation's World Conservation Center, cloud forests comprise only 2.5% of the world's tropical forests. Approximately 25% of them are found in the Andean region. For these reasons, they are considered to be at the top of the list of threatened ecosystems. These ecosystems also play an important role in the protection of water resources - many cities and towns rely of these forests for their drinking water.