[1] The higher elevations in the Pamir-Alay are in the Pamir alpine desert and tundra ecoregion, and heavily glaciated.

To the west, and at lower elevations, is the Alai-Western Tian Shan steppe ecoregion.

Below 1800-2000 meters the desert foothills are characterized by sagebrush (Artemisia), bulbous bluegrass (Poa bulbosa), and sedges (Carex pachystilis).

At higher elevations are meadows and grasslands dominated by fescues (Festuca alaica).

Junipers (Juniperus seravschanica, Juniperus turkestanica, and J. semiglobosa), wild fruit trees (cherry, pears, apples) and nut trees (almonds, pistachios) grow along with steppe grasses and shrubs of Cotoneaster, rose, and honeysuckle (Lonicera).