Freeman's auction house says the 12 flags have been in private hands for more than 150 years and belonged to the late H. Richard Dietrich Jr.
Officials said the 11 flags from the USS Constitution, including a 19-star ensign used from 1816 to 1817, all sold, along with a cannonball from the vessel. The oldest banner, which dates to the late 18th or early 19th century and bears 13 stars and eight stripes, wasn't sold.
The Constitution known as Old Ironsides, is the world's oldest commissioned warship still afloat. It's moored near Boston in Charlestown, Mass.