Trichechus Manatus Latirostris
The Florida manatee lives in near-shore marine, estuarine and fresh waters that are shallow, warm and calm. As herbivores they eat sea grasses and other submerged or floating vegetation.

Where to Find

Because the waters throughout the Rookery Bay National Estuarine Research Reserve provide this essential habitat and food supply, manatees are commonly seen in these waters especially in winter when their population concentrates in the warmest waters available.

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Despite protection under the Endangered Species and Marine Mammal Protection Acts, the manatee population in Florida is at risk. This is partly because human activity in manatee habitat directly correlates with manatee mortality. With one of the largest boating populations in the state, Collier County generally ranks within the top five counties statewide for manatee mortality resulting from collisions with boats.

The reserve works in many ways to provide federal, state and county officials with science-based information on which to base their conservation efforts. In cooperation with USFWS and other partners, the reserve has participated in a long-term monitoring program to identify areas of heavy use by both manatees and boats through aerial surveys. The reserve also provides workshops for coastal law enforcement and natural resource managers through the Coastal Training Program. These efforts have begun to interagency coordination of manatee strandings.

As a member of the Florida -Southwest Region Marine Mammal Stranding Network, the reserve provides trained staff and logistic support to the Florida Fish and Wildlife Research Institute (FWRI), the agency responsible for rescuing stranded, injured or sick manatees around the state. Because they have so much coastline to cover, reserve biologists often serve as first responders who verify the location and status of injured manatees (and other marine mammals), keeping tabs on their whereabouts until more help arrives from FWRI headquarters in Port Charlotte. On January 7, reserve biologists assisted in the recovery of an injured manatee and her calf from the Faka-Union Canal near Port of the Islands in eastern Collier County. Reserve staff transported the manatees to the Miami Sea Aquarium for treatment and rehabilitation until they can be released back into reserve waters in the future.

Visit the Florida Fish and Wildlife Conservation Commission Website to learn more.

Henderson Creek

When Gulf water temperatures drop below 68 degrees, manatees can become cold-stressed and must seek warmer waters. The Faka-Union Canal and Henderson Creek are examples of waterways that provide a freshwater source that is warmer than the Gulf, which is why these locations frequently serve as manatee aggregation areas. It is extremely important for boaters to recognize that inland waterways like these see a significant increase in use by manatees during the winter months and extra caution is necessary when navigating these locations at this time of year. A spring-fed basin at the headwaters of Henderson Creek is the only “No Motor Zone” in Collier County because of its consistent use by manatees as a cold-weather refuge.

Rookery Bay Wildlife: Manatees | National Estuarine Research Reserve
Wildlife at Rookery Bay Research Reserve: Eastern Cottontail Rabbit | National Estuarine Research Reserve

Eastern Cottontail Rabbit

Syivilagus Floridanus
The Eastern Cottontail, Syivilagus floridanus, is the most widely distributed of the rabbits and hares. Best known for its short, fluffy tail which is cottony-white below, the cottontail is grayish-brown above, with white underparts and feet. Its nape is rust-colored. Most active between sunset and dawn, it feeds on plant material. During the day, the cottontail conceals itself in shallow depressions in protected areas called “forms.”

Where to Find

In Rookery Bay Reserve, it is seen in the scrub, pine flatwoods, and open grassy areas, and is a common visitor to the grounds of the Environmental Learning Center. Its cousin, the marsh rabbit, is darker and has shorter ears than the cottontail, and is more commonly associated with wetland habitats both fresh and salt.
Click below to watch a video of a cottontail rabbit foraging in the courtyard at the Environmental Learning Center.

Bottlenosed Dolphin

Tursiops Truncatus
The bottlenosed dolphin is large, grey above, and somewhat paler below. Its Torpedo-shaped body is streamlined for swift movements. Navigating by using a series of clicking sounds that travel throughout the water, the Bottlenosed Dolphin can tell size, shape, and location of objects. This sonar also aids the animal in discovering fish for food.

Where to Find

This dolphin can be seen in Rookery Bay often feeding on mullet, one of its favorite foods.
Rookery Bay Wildlife: Dolphins | National Estuarine Research Reserve
Mammals at Rookery Bay: White Tailed Deer | National Estuarine Research Reserve

White-Tail Deer

One of our largest native mammals, the whitetail deer weighs 150 to 300 lbs. It is tan above with a white belly, noseband and eye ring. Its tail is brown above and white below. When alarmed, the tail is raised, displaying a flash of white communicating danger to other deer. The long slender legs of this deer give it great swiftness, with top speeds of 35 m.p.h. for short distances. It is also a good swimmer. Active at dawn and dusk, it eats large quantities of vegetation.

Where to Find

The white-tail deer is typically found in the pine flatwoods of Rookery Bay Reserve, along Shell Island Road and on Key Island.


Sus Scrofa
Feral hogs, sometimes referred to as “wild boar,” are an invasive exotic species first introduced to Florida by the Spanish in the 1500’s. They are considered nuisances because they tear up the ground while searching for buried food items, both plant and animal. They leave behind scars that resemble the work of a bulldozer. They can also be aggressive – if you see one, give it a wide berth.

Visit the Florida Fish and Wildlife Conservation Commission Website to learn more.

Rookery Bay Wildlife: Wild Pigs | National Estuarine Research Reserve
Mammals at Rookery Bay: Bobcats | National Estuarine Research Reserve


Lynx Rufus
The bobcat gets its name from its short, stubby tail tipped in black. Reaching lengths between 28-49″, the bobcat is substantially larger than a housecat. It is tawny in color and its legs are marked with dark horizontal stripes. Its face has thin lines radiating into a broad cheek ruff. Active early and late in the day, the bobcat typically uses the same hunting paths to prey on small mammals, birds and insects. Bobcats are more commonly observed in this area than panthers, which have tails as long as their bodies but are extremely rare and secretive.
The video below was filmed by reserve staff from an office window.
Mammals at Rookery Bay: Black Bears | National Estuarine Research Reserve


Ursus Americanus Floridanus
The Florida black bear is black with a brown muzzle, weighing up to 400 pounds. Black bears are active during the day, particularly in the early morning and evening hours. Bears roam large areas in search of a mate or food. About 80 percent of a black bear’s diet consists of vegetative matter, including roots, berries and nuts, but they also eat insects and small animals. They have long, sharp claws that enable them to climb trees for food or protection.

Visit the Florida Fish and Wildlife Conservation Commission Website to learn more.

Where to Find

Sharing much of their habitat with people, bears are often considered a nuisance because they raid garbage cans and bird feeders at times when natural food is in short supply. The Florida black bear is listed as a threatened species and has been documented using the upland habitats within Rookery Bay Reserve.


Lutra Canadensis
The river otter is a dark brown mammal with a long slender body and short legs. Its rudder-like tail and webbed feet allow for rapid movement under water. Although aquatic, it runs well on land and may travel several miles over land to reach another body of water. It feeds mostly on fish, but also eats crustaceans, mollusks and small land animals such as mice and reptiles. Intelligent and playful, river otters are active in early morning and evening hours.

Visit the Florida Fish and Wildlife Conservation Commission Website to learn more.

Where to Find

They are typically found in freshwater areas such as river banks, ponds and swamps throughout northern and eastern North America.
Rookery Bay Wildlife: River Otters | National Estuarine Research Reserve
Mammals at Rookery Bay: Florida Panther | National Estuarine Research Reserve

Florida Panther

Puma Concolor Coryi
The Florida panther is one of the most endangered mammals in the U.S. They are light brown or tawny-colored with black whisker patches and a long tail that may be kinked near the end. Florida panthers were over-hunted nearly to extinction until the 1950’s when they were first protected by the State of Florida.

Where to Find

Typically found inland inhabiting hydric pine flatwoods, Florida panthers are frequently observed using habitat in the Reserve as part of their range, as confirmed by both radio collar tracking and wildlife camera imagery.
As part of our listed species monitoring program, Rookery Bay Research Reserve biologists use RECONYX wildlife cameras at a known crocodile nesting site to document nesting and predation. The camera has captured images of many different animals at the nest site, including Florida panther.

The images in this series are are clear enough that panther biologists could possibly identify the individual through scars and other markings, and provide a rare opportunity to observe endangered species behavior. The panther was clearly curious about the camera however, it stayed in view for nearly 30 minutes over the duration of this video.

Explore with Us!

Guided Kayak Tours

Discover Rookery Bay’s extraordinary wildlife on one of our naturalist guided kayak tours. Two-hour guided kayak tours let you explore backwater bays and mangrove forests and provide opportunities to see wildlife such as wading birds, osprey, fish and dolphins.