The affected waters, which span the coastlines of four states, are largely between the mouth of the Mississippi River in Louisiana and Florida's Pensacola Bay, the NOAA said.
The ban took immediate effect and is in place for at least 10 days.
The U.S. Gulf coast is a rich breeding ground for fish, crabs, oysters and shrimp and accounts for about 20 percent of the nation's total commercial seafood production. The shrimp and oyster supply, in particular, is heavily concentrated in the Gulf.
"Balancing economic and health concerns, this order closes just those areas that are affected by oil," NOAA Administrator Jane Lubchenco, said in a statement. "There should be no health risk in seafood currently in the marketplace."
Officials are working to prohibit harvesting from affected areas and to keep oiled seafood off the market.
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