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Over thirty species of birds use Pelican Island as a rookery, roost, feeding ground, or loafing area. Sixteen different species of birds nest on Pelican Island, which include the:

Brown pelican
Wood stork
Great egret
Snowy egret
Reddish egret
Cattle egret
Great blue heron
Little blue heron
Tricolored heron
Green-backed heron
Black-crowned night heron
Double-crested cormorant (resident)
Anhinga
White ibis
American oystercatcher
Common moorhen

Species that nest elsewhere in the refuge or nearby include:

Least tern
Royal tern
Black skimmer
Osprey
 

Summer visitors include:

Roseate spoonbill
Magnificent frigatebird

Wintering birds include:

White pelican
Double-crested cormorant (migratory)
Blue-wing teal
Lesser scaup
Red-breasted merganser
Ring-billed gull
Laughing gull
Forster's tern
Common loon

Endangered species include:

Wood storks
Florida manatee
Green sea turtle
Hawksbill sea turtle
Kemp's ridley sea turtle

Threatened species include:

Loggerhead sea turtle
Eastern indigo snake
Bald eagle
Piping plover


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