It made landfall on October 10 as a Category 4 storm with 155mph winds in Florida’s Panhandle region.
According to officials, the victims were killed by falling trees.
Hurricane Michael was downgraded to a tropical storm as it weakened over Georgia on its way to the Carolinas.
The US National Hurricane Center says that storm-surge warnings are in place between Panama City Beach and Keaton Beach in Florida, and between Ocracoke Inlet and Duck in North Carolina.
Hundreds of thousands of homes and businesses were left without electricity in Florida, Alabama and Georgia.
There are fears for people who ignored evacuation warnings in some of the areas now flooded.
According to Florida officials, a man was killed when he was crushed by a tree in Gadsden County while a child died when a tree fell on a home in Seminole County, Georgia.
The storm earlier reportedly killed at least 13 people as it passed through Central America: six in Honduras, four in Nicaragua and three in El Salvador.
Hurricane Michael made landfall near Mexico Beach, Florida, at around 14:00 on October 10.
Only the unnamed Labor Day hurricane, which hit Florida in 1935, and Hurricane Camille, which struck Mississippi in 1969, made landfall with greater intensity.
The Labor Day storm’s barometric pressure (the lower the number, the stronger the storm) was 892 millibars and Camille’s was 900, while Michael blew in with 919.
Hurricane Michael was so powerful as it swept into Florida that it remained a hurricane as it moved further inland.
Its rapid intensification caught many by surprise, although the storm later weakened.
Only on October 9 Michael was a Category 2 hurricane but by October 10 it had reached borderline category five, the highest level.
More than 370,000 people in Florida were ordered to evacuate but officials believe many ignored the warning.
The storm knocked out power to a quarter of a million homes and businesses, as power lines were smashed by falling trees.
Federal Emergency Management Agency Director Brock Long said at the White House that he was especially concerned about buildings constructed before 2001, and not able to withstand such high winds.
President Donald Trump responded: “We just hope those structures can hold up.”
“And if not, that they’re not in those structures.”
States of emergency have been declared in all or parts of Florida, Alabama, Georgia and North Carolina.
Schools and state offices in the area are to remain shut this week and Florida has activated 3,500 National Guard troops.
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