Pennsylvania’s forests are filled with maple, ash, poplar, oak, walnut, pine, beech, and linden trees, along with sassafras, weeping willow, sycamore, and balsam fir (Abies fraseri). Red pine and paper birch are found in the north while the sweet gum is dominant in the extreme southwest. Mountain laurel, the state flower, New Jersey tea, June-berry, dotted hawthorn, and various dogwoods are among the shrubs and small trees found in most parts of the state. Dewberry, wild columbine, wintergreen, and wild ginger are also common. In 2003, the small whorled pogonia and Virginia spirea were classified as threatened, with the northeastern bulrush as endangered.

Numerous mammals can be found in Pennsylvania. Among them the white-tailed deer (the state animal), black bear, opossum, red and gray foxes, muskrat, snowshoe hare, raccoon, common cottontail, mink, and red, gray, fox, and flying squirrels. Native amphibians include the hellbender, Fowler's toad, and the tree, cricket, and true frogs.  among reptilian species are the five-lined and black skinks and five varieties of lizard. The ruffed grouse, a common game species, is the official state bird. Other game birds are the wood dove, bobwhite quail, ring-necked pheasant, and mallard and black ducks. More than 170 types of fish have been identified in Pennsylvania, with brown and brook trout, grass pickerel, bigeye chub, pirate perch, and white bass among the common native varieties.

In 2003 14 species, including the Indiana bat, bald eagle, orangefoot pimpleback pearly mussel, dwarf wedgemussel, and pink mucket pearlymussel were listed as threatened or endangered.