The Florida Fish and Wildlife Conservation Commission, charged with managing the state's fish and wildlife resources, counted 5,076 manatees, 1,269 more than the record 3,807 counted last year, the officials said.
The two years of increases "would indicate that populations are doing better and we're seeing some type of increase," manatee research scientist Holly Edwards of the commission's Fish and Wildlife Research Institute, told the Sarasota (Fla.) Herald-Tribune.
Recent cold weather played a role in the count, officials said.
"We've known for a very long time that the results of these surveys are very dependent on weather," Edwards told the newspaper. "This was an exceptional year, weather-wise, and it really pushed a lot of manatees into the areas we're counting."
The unusual cold sent manatees to warm water refuges, such as warm springs and power plant discharge canals, officials said.
While the overall annual count rose, the endangered mammals also suffered the deadliest year on record in 2009 as state wildlife biologists documented 429 fatalities -- including 97 killed by boat strikes, 114 dying shortly after birth and 56 dying of cold stress, officials said.
Manatees are large, plant-eating aquatic mammals sometimes known as sea cows. They are noted for their friendly nature and paddle-like flippers.