One is growing off the Big Bend area in the northern part of the state, while the other is shrinking north of the Florida Keys.
The blooms endanger sea life by stealing oxygen from the water. The dying algae also feed other more toxic blooms such as red tide, which can cause breathing problems in people.
Earlier photos indicated both blooms originated along the coast and concentrated farther from shore.
Scientists at the University of South Florida in Tampa suspect they are related to river discharge that comes into Charlotte Harbor and moves offshore.
Samples have been taken from the northern mass of dark water off the Big Bend area, where the Florida peninsula meets the Panhandle.
Scientists from Mote Marine Laboratory in Sarasota found a diatom common in lower concentrations in coastal waters. Diatoms are microscopic aquatic algae that make up most of the phytoplankton in the Gulf