New York has some 150 species of trees and 600 species of mammals, birds, amphibians and reptiles. Popular trees found in the Atlantic shore areas are  post and willow oak, laurel magnolia, sweet gum, and hop trees while oak, hickory, and chestnut dominate the Hudson and Mohawk valleys and the Great Lakes Plain. Birch, beech, basswood, white oak, and commercially valuable maple are found on the Appalachian Plateau and in the foothills of the Adirondack Mountains. Red and black spruce, balsam fir, and mountain ash, as well as white pine and maple are found in plenty in the Adirondacks and Catskills.

Common meadow flowers include several types of rose (the state flower), along with dandelion, Queen Anne's lace, goldenrod, and black-eyed Susan. Wild sarsaparilla, Solomon's seal, Indian pipe, bunchberry, and goldthread flourish amid the forests. Six plant species including the sandplain gerardia, American hart's-tongue fern, and Leedy's roseroot were listed as threatened or endangered in 2003.

Some 600 species of mammals, birds, amphibians, and reptiles are found in New York, of which more than 450 species are common. The more popular ones include many mouse species, the snowshoe hare, common and New England cottontails, woodchuck, squirrel, muskrat, and raccoon. More than 260 bird species have been observed, the most common being the crow, hawk, and several types of woodpecker. The common toad, newt, and several species of frog and salamander are found in New York waters. Garter snakes, water snakes, grass snakes, and milk snakes are common; rattlesnakes formerly thrived in the Adirondacks. There are 210 known species of fish; 130 species are found in the Hudson, 120 in the Lake Ontario watershed.

In 2003, twenty animal species were classified as threatened or endangered. Among those endangered are the Indiana bat, bald eagle, shortnose sturgeon, piping plover, three species of whale, Karner blue butterfly, and five species of turtle.