One night in 1862, as the Civil War raged, an enslaved mariner named Robert Smalls seized an opportunity.

When the enlisted crew of a Confederate steamer disembarked for a night of carousing in Charleston, S.C., Mr. Smalls, the ship’s pilot, gathered his family and the other enslaved sailors and their families. He then steered the ship for a dramatic escape past heavy fortifications to Union-controlled waters and freedom.

Disguised in a top hat and a Confederate captain’s long overcoat, Mr. Smalls gave the passcodes at each of five Confederate forts and, once past the reach of cannon fire, hoisted a white flag of sewn-together bedsheets that his wife Hannah had made — delivering the ship to Union forces.

Mr. Smalls and the crew had lined the bottom of the boat with explosives to detonate rather than be recaptured and face execution.

Now Mr. Smalls will be immortalized on a U.S. Navy warship named after him, as will Marie Tharp, a pioneering ocean geologist. Both are receiving broader recognition under a Pentagon program to rid military installations and other property of Confederate ties.

The Naming Commission, a committee created by Congress in response to a public backlash against Confederate memorials in the wake of the 2020 murder of George Floyd, identified two ships to be rechristened in the Navy’s fleet.

One, a warship deployed in the waters off Japan, called the U.S.S. Chancellorsville after the Confederate Civil War victory in Virginia, will be renamed the U.S.S. Robert Smalls.

The other, a Pathfinder-class oceanographic survey ship called the U.S.N.S. Maury, was named after Matthew Fontaine Maury, a U.S. Navy commander who resigned in 1861 to join the Confederate Navy during the Civil War and who is known as “Pathfinder of the Seas” for his work charting the global paths of ocean currents. It will be rechristened the U.S.N.S. Marie Tharp, after the ocean cartographer, who helped document the phenomenon of continental drift.

When the Naming Commission informed the Navy that it would have four assets to rename — two buildings at the Naval Academy in Annapolis, Md., and two ships — dozens of suggestions flooded Secretary of the Navy Carlos Del Toro’s office, said Tralene Hunston, a civilian employee in the public affairs office.

The Navy is planning namesake ceremonies that do not disrupt operations of either ship, Ms. Hunston said.

The ships were renamed after two people who “have historically been overlooked, but leveled significant impact on not just our Navy, but also the nation,” Mr. Del Toro said in emailed comments to The New York Times.

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The vessels’ renaming is part of a broader Pentagon project to grapple with a legacy that for more than a century has paid homage to Confederate victories and leaders.

Naming Army bases and other military property, and erecting monuments and memorials, to honor the Confederacy was part of a campaign by the children of Confederate soldiers “to reimagine their fathers as not the villains of a treasonous war for slavery but instead for the Southern way of life,” said Michel Paradis, a lecturer at Columbia University.

President Woodrow Wilson, an ardent segregationist, saw granting the requests to honor Confederate soldiers as a good way to rally support among his southern base during a draft for World War I, Paradis said.

In the protests that broke out across the U.S. after Mr. Floyd’s death in the summer of 2020, demonstrators took down dozens of Confederate memorials and monuments. That summer, Congress voted to expunge from Defense Department assets “names, symbols, displays, monuments and paraphernalia” that commemorate the Confederate States of America. The same legislation established the Naming Commission, which quickly proposed new names for nine Army installations in the South.

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