There are 124 native tree species in Indiana. It includes 17 varieties of oak, as well as black walnut, sycamore, and tulip tree (yellow poplar), the state tree. Fruit trees like apple, cherry, peach, and pear are common. American elderberry and bittersweet are common shrubs, while various jack-in-the-pulpits and spring beauties are among the indigenous wild flowers. The peony is the state flower. As of August 2003, Mead's milkweed and Pitcher's thistle were considered threatened and Short's goldenrod and running buffalo clover were considered endangered.

Among the various animals found in Indiana, the red fox is the common carnivorous mammal. Other native mammals are the common cottontail, muskrat, raccoon, opossum, and several types of squirrel. Many waterfowl and marsh birds, including the black duck and great blue heron, inhabit northern Indiana, while the field sparrow, yellow warbler, and red-headed woodpecker nest in central Indiana.

The US Fish and Wildlife Service listed 25 Indiana animal species as threatened or endangered as of August 2003. Among these are the bald eagle, Indiana and gray bats, gray wolf, piping plover, and two species of butterfly.