Bhutan has six ecoregions as shown in the figure below (from north to south):
- Eastern Himalayan alpine shrub and meadows (Blue)
- Eastern Himalayan subalpine conifer forests (Aqua)
- Eastern Himalayan broadleaf forests (Light Yellow)
- Himalayan subtropical pine forests (Sky Blue)
- Himalayan subtropical broadleaf forests (Mid-yellow)
- Terai-Duar savanna and grasslands (Dark Yellow)
The transistion from the Himalayan subtropical broadleaf forests (6) ecoregion to the Brahmaputra Valley semi-evergreen forests ecoregion of northern Indian (at the bottom of the figure) approximately follows the southern border of Bhutan.
The Eastern Himalayan Alpine Shrub and Meadows represent the alpine scrub and meadow habitat along the Inner Himalayas to the east of the Kali Gandaki River in central Nepal. Within it are the tallest mountains in the world-Everest, Makalu, Dhaulagiri, and Jomalhari-which tower far above the Gangetic Plains. The alpine scrub and meadows in the eastern Himalayas are nested between the treeline at 4,000 meters (m) and the snowline at about 5,500 m and extend from the deep Kali Gandaki gorge through Bhutan and India's northeastern state of Arunachal Pradesh, to northern Myanmar.
The Eastern Himalayan Alpine Shrub and Meadows ecoregion supports one of the world's richest alpine floral displays that becomes vividly apparent during the spring and summer when the meadows explode into a riot of color from the contrasting blue, purple, yellow, pink, and red flowers of alpine herbs. Rhododendrons characterize the alpine scrub habitat closer to treeline. The tall, bright-yellow flower stalk of the noble rhubarb, Rheum nobile (Polygonaceae), stands above all the low herbs and shrubs like a beacon, visible from across the valleys of the high Himalayan slopes.
The plant richness in this ecoregion sitting at the top of the world is estimated at more than 7,000 species, a number that is three times what is estimated for the other alpine meadows in the Himalayas. In fact, from among the Indo-Pacific ecoregions, only the famous rain forests of Borneo are estimated to have a richer flora. Within the species-rich landscape are hotspots of endemism, created by the varied topography, which results in very localized climatic variations and high rainfall, enhancing the ability of specialized plant communities to evolve. Therefore, the ecoregion boasts the record for a plant growing at the highest elevation in the world: Arenaria bryophylla, a small, dense, tufted cushion-forming plant with small, stalkless flowers, was recorded at an astonishing 6,180 m by A. F. R. Wollaston.
The ecoregion has fourteen protected areas that cover more than 11,680 km2, including several-such as Annapurna, Makalu Barun, Sagarmatha, Jigme Dorgi, and Sakteng-that exceed 1,000 km2 (or, as in the case of Annapurna and Jigme Dorji, 2,500 km2). Although the total area protected represents about 30 percent of the ecoregion's area, the reserves are inequitably distributed. Most of the protected areas are in Nepal and Bhutan, whereas the eastern section of the ecoregion, especially in Myanmar, receives little or no formal protection. Because of the high species turnover along the east-west axis, more equitable protection is necessary for better representation of the ecoregion's biodiversity. Moreover, about half of the areas that lie within the existing protected areas represent bare rock and areas covered with permanent ice, not very important habitat for biodiversity conservation.
The ecoregion represents the belt of conifer forest between 3,000 and 4,000 meters, from east of the Kali Gandaki River in Nepal through Bhutan and into the state of Arunachal Pradesh, in India. These forests usually are confined to the steeper, rocky, north-facing slopes and therefore are inaccessible to human habitation and cultivation.
The Eastern Himalayan Sub-Alpine Conifer Forests represent the transition from the forested ecoregions of the Himalayas to treeless alpine meadows and boulder-strewn alpine screes. Their ecological role within the interconnected Himalayan ecosystem, which extends from the alluvial grasslands along the foothills to the high alpine meadows, makes the forests of this ecoregion a conservation priority. Conservation of the Himalayan biodiversity is contingent on protecting the interconnected processes among the Himalayan ecosystems. For instance, several Himalayan birds and mammals exhibit altitudinal seasonal migrations and depend on contiguous habitats that permit these movements. The integrity of the watersheds of the rivers that originate in the high mountains of this majestic range depends on the intactness of habitat, from the high elevations to the lowlands. If any of the habitat layers are lost or degraded, these processes will also be disrupted.
The ecoregion straddles the transition from the southern Indo-Malayan to the northern Palearctic fauna. Here tigers yield to snow leopards, and sambar are replaced by blue sheep. But the ecoregion also has its own specialized flora and fauna, such as the musk deer and red panda, which are limited to these mature temperate conifer forests.
This ecoregion represents the band of temperate broadleaf forest between 2,000 and 3,000 meters, stretching from the deep Kali Gandaki River gorge in central Nepal, eastward through Bhutan, into India's eastern states of Arunachal Pradesh and Nagaland.
The Eastern Himalayan Broadleaf Forests is one of the few Indo-Pacific ecoregions that is globally outstanding for both species richness and levels of endemism. The eastern Himalayas are a crossroads of the Indo-Malayan, Indo-Chinese, Sino-Himalayan, and East Asiatic floras as well as several ancient Gondwana relicts that have taken refuge here. Overall, this ecoregion is a biodiversity hotspot for rhododendrons and oaks; for instance, Sikkim has more than fifty rhododendron species, and there are more than sixty species in Bhutan.
In addition to the outstanding levels of species diversity and endemism, the ecoregion also plays an important role in maintaining altitudinal connectivity between the habitat types that make up the larger Himalayan ecosystem. Several birds and mammals exhibit altitudinal seasonal migrations and depend on contiguous habitat up and down the steep Himalayan slopes for unhindered movements. Habitat continuity and intactness are also essential to maintain the integrity of watersheds along these steep slopes. If any of the habitat layers, from the Terai and Duar grasslands along the foothills through the broadleaf forests and conifers to the alpine meadows in the high mountains, are lost or degraded, these processes will be disrupted. For instance, several bird species are found in the temperate broadleaf forests of Bhutan where the habitat is more intact and continuous with the subtropical broadleaf forests lower down, but in Nepal where the habitat continuity has been disrupted, these same birds have limited ranges.
The fifteen protected areas that extend into the ecoregion cover about 5,800 kilometers2 (7 percent) of the ecoregion. With the exception of Namdapha, none exceed 1,000 kilometers2. However, there are several very large reserves that overlap across several ecoregions, although only parts of the reserves are represented in this one. Examples include Thrumsing La, Jigme Dorji, and Black Mountains national parks in Bhutan. The Jigme Dorji National Park exceeds 4,000 kilometers2 and sprawls across three ecoregions to include the alpine meadows, sub-alpine conifer forests, and temperate broadleaf forests represented by this ecoregion. Two others, Kulong Chu and Black Mountains, exceed 1,000 kilometers2, and Cha Yu, Makalu-Barun, Mehao, and Thrumsing La are more than 500 kilometers2.
Bhutan recently revised its protected area system to link the existing reserves. Plans to develop similar linkages through conservation landscapes have been proposed in the other areas in the eastern Himalayas. These plans use ecoregions as basic conservation units for representation of biodiversity.
The subtropical pine forests represented by this ecoregion extend as a long, disjunct strip from Pakistan in the west, through the states of Jammu and Kashmir, Himachal Pradesh, and Uttar Pradesh in northern India, into Nepal and Bhutan. Although Champion and Seth indicate the presence of large areas of Chir pine in Arunachal Pradesh, the easternmost extent of large areas of Chir pine is in Bhutan.
The Himalayan Subtropical Pine Forests are the largest in the Indo-Pacific region. They stretch throughout most of the 3,000-kilometer length of this the world's youngest and highest mountain range. Some scientists believe that climate change and human disturbance are causing the lower-elevation oak forests to be gradually degraded and invaded by the drought-resistant Chir pine (Pinus roxburghii), the dominant species in these subtropical pine forests. Biologically, the ecoregion does not harbor exceptionally high levels of species richness or endemism, but it is a distinct facet of the region's biodiversity that should be represented in a comprehensive conservation portfolio.
More than half of this ecoregion's natural habitat has been cleared or degraded. In central and eastern Nepal, terraced agriculture plots, especially between 1,000 and 2,000 m, have replaced nearly all the natural forest. Other than in the less populated western regions, little natural forest remains in Nepal. Similarly, habitat loss is widespread in Pakistan, Jammu and Kashmir, and Himachal Pradesh and Uttar Pradesh states in India. The few larger blocks of remaining habitat blocks are now found in Bhutan.
This ecoregion represents the east-west-directed band of Himalayan subtropical broadleaf forests along the Siwaliks or Outer Himalayan Range, lying between 500 and 1,000 meters (m). The ecoregion achieves its greatest coverage in the middle hills of central Nepal, but the long, narrow ecoregion extends through Darjeeling into Bhutan and also into the Indian State of Uttar Pradesh. The Kali Gandaki River, which has gouged the world's deepest river valley through the Himalayan Range, bisects the ecoregion.
The Himalayan Subtropical Broadleaf Forests ecoregion includes several forest types along its length as it traverses an east to west moisture gradient. The forest types include Dodonea scrub, subtropical dry evergreen forests of Olea cuspidata, northern dry mixed deciduous forests, dry Siwalik sal (Shorea robusta) forests, moist mixed deciduous forests, subtropical broadleaf wet hill forests, northern tropical semi-evergreen forests, and northern tropical wet evergreen forests.
The ecoregion also forms a critical link in the chain of interconnected Himalayan ecosystems that extend from the Terai and Duar grasslands along the foothills to the high alpine meadows at the top of the world's highest mountain range. For instance, several Himalayan birds and mammals exhibit seasonal altitudinal migrations and depend on contiguous habitat to permit these movements. Therefore, conservation actions in the Himalayas must pay due attention to habitat connectivity because degradation or loss of a habitat type along this chain will disrupt these important ecological processes.
The Terai-Duar Savanna and Grasslands ecoregion sits at the base of the Himalayas, the world's youngest and tallest mountain range. About 25 kilometers wide, this narrow lowland ecoregion is a continuation of the Gangetic Plain. The ecoregion stretches from southern Nepal's Terai, Bhabar, and Dun Valleys eastward to Banke and covers the Dang and Deokhuri Valleys along the Rapti River. A small portion reaches into Bhutan, and each end crosses the border into India's states of Uttar Pradesh and Bihar.
This ecoregion contains the highest densities of tigers, rhinos, and ungulates in Asia.
One of the features that elevates it to the Global 200 ecoregion is the diversity of ungulate species and extremely high levels of ungulate biomass recorded in riverine grasslands and grassland-forest mosaics.
The world's tallest grasslands, found in this ecoregion, are the analogue of the world's tallest forests and are a phenomenon unto themselves. Very tall grasslands are rare worldwide in comparison with short grasslands and are the most threatened. Tall grasslands are indicators of mesic or wet conditions and nutrient-rich soils. Most have been converted to agricultural use.
Ecoregions are areas that:
 share a large majority of their species and ecological dynamics;
 share similar environmental conditions; and,
 interact ecologically in ways that are critical for their long-term persistence.
Scientists at the World Wildlife Fund (WWF), have established a classification system that divides the world in 867 terrestrial ecoregions, 426 freshwater ecoregions and 229 marine ecoregions that reflect the distribution of a broad range of fauna and flora across the entire planet.