For years now, researchers have believed that the manatee population was somewhere between 2,000 and 3,000 animals. The last aerial survey of the Florida manatee population was done in February 2004. The survey showed a population count of 2,568 manatees. A synoptic survey is a statewide aerial survey designed to get a head count of individual manatees. The success of synoptic surveys is very dependent on weather conditions. If the weather is cold and clear, then manatees are gathered around warm water sites, making it easier to get a "nose" count. Synoptic surveys are not the most reliable way to determine overall manatee population because so much depends on weather conditions, but they are the only available method at present.

Many researchers agree that in two areas in the state Florida the manatee population is growing, through both reproduction and migration of manatees from other areas of the state. These two areas, Blue Spring in Volusia County (known by researchers as the Upper St. Johns River) and Crystal River/Kings Bay in Citrus County (known as the northwest region), have been protected areas for over 30 years and are relatively rural areas with less boat traffic. Blue Spring is a no-entry zone (refuge) and several no-entry zones (sanctuaries) have been established in Kings Bay. Both sites also have substantial slow speed zones in surrounding waterways. It is believed that, because of these factors, these two sub-populations have increased. It is important to note, however, that these two groups combined comprise only about 16% of Florida’s total manatee population.

No one yet knows the status of the two remaining manatee regional sub-populations. The data available from these regions is not sufficient to make a statistically reliable estimate of the population trend. The East Coast and Southwest manatee populations may be stable at best or may be declining. This is important because these two regional sub-populations make up the remaining 84% (the vast majority) of the manatee population in Florida.

In 2003, a population model was released by the U.S. Geological Survey that predicted an extremely grave situation confronting the manatee in both the Southwest and Atlantic regions where the vast majority of manatees are found. It states, “In the absence of any new management action, that is, if boat mortality rates continue to increase at the rates observed since 1992, the situation in the Atlantic and Southwest regions is dire, with no chance of meeting recovery criteria within 100 years.”

Actual manatee fossils found all over the world go back as far as 60 million years. Modern manatees evolved from four-footed land mammals. Manatee fossils found in Florida’s springs date back about 45 million years.