Florida hosts many types of fauna. From coral reefs of the Florida Keys to the cypress swamps of the Panhandle, the state's diverse habitats are home to a variety of wildlife. Florida is among the top five states in terms of endemic species. There are over 700 terrestrial animals, 200 freshwater fish species, 1,000 marine fish and thousands of terrestrial insects and other invertebrates that inhabit the state. Florida's peninsular geography spans from subtropical to tropical zones, which, combined with its distinctive geology and climate, contribute to habitat diversity and an array of species. The native wildlife that exists in the state are of temperate and tropical origin.

Florida once had a large number of species that formerly occupied the state in prehistoric and historic times, but became locally extinct or extirpated; such as the Florida short-faced bear, Florida black wolf, Dire wolf, Dexteria floridana, Florida bog lemming, Long-nosed peccary, Caribbean monk seal, Carolina parakeet, Great auk, Passenger pigeon, Ivory-billed woodpecker, Bachman's warbler, Dusky seaside sparrow, Pallid beach mouse, Chadwick Beach cotton mouse, Goff's pocket gopher, California condor, Island raccoon, Northern short-tailed shrew, magpie, indigo snake, northern leopard frog, porcupine, great black hawk, red wolf, elk, hog-nosed skunk, gray wolf, underwood's bonneted bat, Pristine mustached bat, white-tailed jackrabbit, band-tailed pigeon, jaguar, margay, jabiru, ocelot, ghost-faced bat, collared peccary, great-tailed grackle, ringed kingfisher, common opossum, gray-breasted crake, Northern jacana, yellow-headed caracara, ruffed grouse, Southern lapwing and greater prairie chicken.

Aquatic mammal species are represented by the bottlenose dolphin, short-finned pilot whale, North Atlantic right whale and West Indian manatee. Terrestrial species; the Florida panther, northern river otter, mink, eastern cottontail rabbit, marsh rabbit, raccoon, striped skunk, squirrel, white-tailed deer, bobcat, red fox, gray fox, coyote, beaver, Florida black bear, nine-banded armadillo, and Virginia opossum. The only known calving area for the northern right whale is off the coasts of Florida and Georgia.

The native bear population has risen from a historic low of 300 in the 1970s, to 3,000 in 2011. In Paynes Prairie Preserve State Park, The plains bison were reintroduced to the park from the Wichita Mountains Wildlife Refuge in 1975, as part of the park service goal of restoring Florida's natural resources to pre-European settler conditions; they roamed this area until the late 18th century. When bison sightings occur, they usually appear along the Cone's Dike trail. The herd was reduced from thirty-five to seven individuals in the mid-1980s after an outbreak of Brucellosis. In the late 1990s, the herd was again reduced after inbreeding concerns. The buffalo herd reached a peak of 70 animals in 2011. The park began culling excessive animals in 2012, allowing a target population of about 8 to 10 bison to be free to roam the Florida prairie.

Bird species include the Peregrine falcon, bald eagle, American flamingo, crested caracara, snail kite, osprey, white and brown pelicans, sea gulls, whooping and sandhill cranes, roseate spoonbill, American white ibis, Florida scrub jay (state endemic), and others. One subspecies of wild turkey, Meleagris gallopavo, namely subspecies osceola, is found only in Florida. The state is a wintering location for many species of eastern North American birds.

There have been small numbers of several new species normally native to cooler areas to the north: snowy owls, snow buntings, harlequin ducks, and razorbills. These have been seen in the northern part of the state.

The American flamingo was also found in South Florida, which was likely the northernmost extent of its distribution. The study also indicated that these flamingos may be increasing in population and reclaiming their lost land. Large flocks of flamingos are still known to visit Florida from time to time, most notably in 2014, when a very large flock of over 147 flamingos temporarily stayed at Stormwater Treatment Area 2, on Lake Okeechobee, with a few returning the following year. From a distance, untrained eyes can also confuse it with the roseate spoonbill.

Indigenous reptiles include Eastern diamondback, pygmy rattlesnakes, gopher tortoise, green and leatherback sea turtles, and eastern indigo snake and eastern fence lizard. In 2012, there were about one million American alligators and 1,500 crocodiles. The highest species of freshwater turtles (consisting of 13 species) in Florida occur in the Escambia River basin. Other basins, particularly in the panhandle and northern central of the state contain 12 species. North Florida has the third richest turtle fauna in the world. The state's native species has 31 turtles, 15 lizards, 2 crocodilians, and 40 snakes.