[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).

cuspidata, Tsuga dumosa, Taxus sumatrana, Betula utilis, Alnus nepalensis, Betula alnoides, Betula utilis, Picea brachytyla, Juglans regia, Larix gmelinii, Larix sibirica, Larix × czekanowskii, Betula dahurica, Betula pendula, Pinus koraiensis, Pinus sibirica, Pinus sylvestris, Picea obovata, Abies sibirica, Quercus acutissima, Quercus mongolica, Ginkgo biloba, Prunus serrulata, Prunus padus, Tilia amurensis, Salix babylonica, Acer palmatum, Populus tremula, Ulmus davidiana, Ulmus pumila, Pinus pumila, Haloxylon ammodendron, Elaeagnus angustifolia, Tamarix ramosissima, Prunus sibirica, Cathaya argyrophylla, Taiwania cryptomerioides, Cyathea spinulosa, Sassafras tzumu, Davidia involucrata, Metasequoia glyptostroboides, Glyptostrobus pensilis, Castanea mollissima, Quercus myrsinifolia, Quercus acuta, Machilus thunbergii, Tetracentron, Cercidiphyllum japonicum, Emmenopterys henryi, Eucommia ulmoides, Ziziphus spina-christi, Ziziphus nummularia, Olea europaea, Balanites aegyptiaca, Cupressus sempervirens, Vachellia tortilis, Salix alba, Populus nigra, Quercus coccifera, Quercus ilex, Quercus pubescens, Pistacia terebinthus, Pinus pinea, Pinus nigra, Ceratonia siliqua, Arbutus unedo, Erica arborea, Laurus nobilis, Vachellia flava, Prosopis cineraria, Pinus halepensis, Toona ciliata, Aerva javanica, Prunus amygdalus, Corylus avellana, Pistacia atlantica, Quercus brantii, Quercus robur, Quercus petraea, Picea abies, Abies alba, Alnus glutinosa, Fagus sylvatica, Taxus baccata, Acer pseudoplatanus, Malus sylvestris, Viburnum lantana, Fraxinus excelsior, Tilia cordata, Aesculus hippocastanum, Rhamnus cathartica, Ulmus glabra, Ulmus minor, Populus alba grow along with steppe grasses and shrubs of Cotoneaster, rose, and honeysuckle (Lonicera).