The reasons for this are the long-term geologic stability of the region, its long ridges and valleys which serve both as barrier and corridors, and their general north-south alignment which allowed habitats to shift southward during ice ages.

The mountains also contain a large variety of diverse landscapes, microclimates and soils all constituting microhabitats allowing many refugia areas and relict species to survive and thrive.

In terms of biodiversity, the only comparable temperate deciduous forest regions in the world are in central China, Japan, and in the Caucasus Mountains.

Typical trees of these forests are sugar maple (Acer saccharum), American beech (Fagus grandifolia), eastern hemlock (Tsuga canadensis), Carolina silverbell (Halesia tetraptera), tulip poplar (Liriodendron tulipifera), red maple (Acer rubrum), white oak (Quercus alba), northern red oak (Quercus rubra), yellow birch (Betula alleghaniensis), yellow buckeye (Aesculus flava), and basswood (Tilia americana).

[5] Southern Appalachian low-elevation pine forests occur on a variety of topographic and landscape positions, including ridgetops, upper- and mid-slopes, and in lower elevations (generally below 2,300 feet (700 m)) such as mountain valleys.

The shrub layer may be well-developed, with hillside blueberry (Vaccinium pallidum), black huckleberry (Gaylussacia baccata), or other acid-tolerant species most characteristic.

Flowering dogwood (Cornus florida), sourwood (Oxydendrum arboreum), sassafras (Sassafras albidum), and blackgum (Nyssa sylvatica) live in the midstory and hillside blueberry (Vaccinium pallidum), black huckleberry (Gaylussacia baccata), and mountain laurel (Kalmia latifolia) are common in the understory, where they can form a dense layer.

[5][12] Northeastern interior dry–mesic oak forests cover large areas at low and middle elevations, typically on flat to gently rolling terrain.

[14] Montane oak forests occur on exposed ridges and on south- to west-facing slopes at middle elevations.

Dead wood, ericaceous shrubs, and a thick layer of poorly decomposed plant litter make this habitat very fire-prone.

[5][16] Northern hardwood forests occur in cool, mesic habitats found above 4,500 feet (1,400 m) on north- and east-facing slopes of the southern Appalachians.

Sugar maple (Acer saccharum), beech (Fagus grandifolia), yellow birch (Betula alleghaniensis), and yellow buckeye (Aesculus flava) dominate but are sometimes joined by the conifers eastern hemlock (Tsuga canadensis), eastern white pine (Pinus strobus), and red spruce (Picea rubens).

These occur only on the highest peaks and ridges, where the soils are poor, the growing season short, and moisture comes from rain, snow, and fog.

[5] Appalachian balds are areas covered by native grasses or dense shrubs that occur only on some high-elevation summits and slopes.

Sods is a term used in the Allegheny Mountains of eastern West Virginia for a mountaintop meadow or bog, in an area that is otherwise generally forested.

[21] Endangered or threatened species of the Appalachians include some snails and salamanders, the red wolf (Canis rufus) and the spruce-fir moss spider (Microhexura montivaga).

The spruce and fir forests of the highlands have been logged particularly intensively and in many cases have not regenerated leaving areas of Appalachian balds heath.

Plants and animals are also threatened by introduced species including the gypsy moth (Lymantria dispar), spruce budworm (Choristoneura fumiferana), hemlock woolly adelgid (Adelges tsugae), balsam woolly adelgid (A. piceae) and the Discula destructiva that affects dogwoods and is similar to chestnut blight.