Bhutan is one of the top ten biodiversity "hotspots" in the world. Bhutan has five climatic zones within its mountainous borders starting at the tropical forests near India and up to the alpine regions. More than 600 species of birds are found in Bhutan. Bird watchers particularly enjoy viewing the migratory Black-necked Cranes that come to rest in Phobjikha Valley starting in autumn. These auspicious birds are known to circle the monastery three times before landing in the marsh. Bhutan offers one of the most populated wetland habitats for these rare birds. Another nearly extinct species is the White-bellied Heron. It is said that only 200 of these birds exist in the world, and Bhutan is the home for many of them.

Bhutan is considered a Rhododendron sanctuary. Many wildflowers dapple the forests canopied with oak, elm, and pines. On one trek, hikers counted 10 different species of mushrooms. Bhutan's national flower, the blue poppy, is a sight to see when blooming in May and June.