The Appalachian Trail is home to literally thousands of species of plants and animals, including 2,000 distinct rare, threatened, endangered, and sensitive plant and animal species.

Animals

The American black bear (Ursus americanus) is the largest omnivore that may be encountered on the trail, and it inhabits all regions of the Appalachians. However, bear sightings on the trail are uncommon, and confrontations rarer still, as black bears typically avoid humans and can usually be frightened away by loud noises. Other hazards include venomous snakes, including the Eastern timber rattlesnake and copperhead, which are common along the trail. Both snakes are generally found in drier, rockier sections of the trail; the copperhead's range extends north to around the New Jersey-New York state line, while rattlesnakes are commonly found along the trail in Connecticut and have been reported, although rarely, as far north as New Hampshire. Other large fauna include deer; elk, reintroduced in the Smoky Mountains; and moose, which live as far south as Massachusetts but are more commonly seen in Maine.

For most hikers, the most persistent pests along the trail are mice and bugs. Mice inhabit shelters and are a greater threat to hiker food than bears. The bugs are a persistent hazard, but are particularly bad in the northern stretches of the trail [citation needed]. Connecticut, Massachusetts, and New York have notoriously bad mosquitoes, but the worst section of the trail for bugs is in the lowlands of Maine [citation needed]. The northern hardwood and boreal forest of Maine is perfect for mosquitoes and tiny, pesky black flies to breed. Numerous lakes, rivers, and streams provide the perfect habitat for biting insects to breed and hatch, especially in late spring and early summer.

In the southern portions of the trail, mosquitoes, no-see-em and other biting flies are less of a nuisance because there are fewer mountain lakes and ponds. In addition, the lack of great seasonal changes in the South keeps the onslaught of these biting insects down. The continental glaciations that carved so many lakes in the northeast stopped near the Delaware Water Gap, leaving the southern mountains with fewer holes to be filled by rain.

Plants

Plant life along the trail is varied. The trail passes through several different biomes from south to north, and the climate changes significantly, particularly dependent upon elevation. In the south, lowland forests consist mainly of second-growth; nearly the entire trail has been logged at one time or another. There are, however, a few old growth locations along the trail, such as Sages Ravine in Massachusetts and The Hermitage, near Gulf Hagas in Maine. In the south, the forest is dominated by hardwoods, including oak and tulip trees, also known as yellow poplar. Further north, tulip trees are gradually replaced by maples and birches. Oaks begin to disappear in Massachusetts. By Vermont, the lowland forest is made up of maples, birch and beech, which provide spectacular foliage displays for hikers in September and October. While the vast majority of lowland forest south of the White Mountains is hardwood, many areas have some coniferous trees as well, and in Maine, these often grow at low elevations.

There is a drastic change between the lowland and subalpine, evergreen forest, as well as another, higher break, at tree line, above which only hardy alpine plants grow. The sub-alpine region is far more prevalent along the trail than true alpine conditions. While it mainly exists in the north, a few mountains in the south have subalpine environments. These include the Great Smoky Mountains, where sub-alpine environments only begin around 6000 feet in elevation, the Unaka and Roan Ranges on the North Carolina-Tennessee border, where sub-alpine growth descends below 6000 feet, and Mount Rogers and the Grayson Highlands in Virginia, where there is some alpine growth above 5000 feet. Some high mountains in the south are also balds, due to fires or grazing in recent centuries, or perhaps due to thin, sandy soils. Several balds are sprouting trees, and on some, the National Forest service actually mows the grasses periodically in order to keep the bald open. Mostly in the mid summer to late fall.