In 1863 Smalls was appointed captain of Planter, the first black man to command a United States ship, and served in that position until 1866.

At 04:00 on 13 May 1862, while her captain, C. J. Relyea, was absent on shore, Robert Smalls, a slave who was Planter's helmsman (the title "pilot" being reserved for white men trained in navigation of rivers,) quietly took the ship from the wharf, and with a Confederate flag flying, steamed past the successive Confederate forts.

In addition to the cargo of artillery and explosives, Smalls brought Flag officer Samuel Francis Du Pont valuable intelligence, including word that the Confederates had abandoned defensive positions on the Stono River.

The United States Senate and House of Representatives passed a private bill on 30 May 1862, granting Robert Smalls and his African-American crew one half of the value of Planter and her cargo as prize money.

[citation needed] Du Pont took Planter into the Union Navy and placed her under command of Acting Master Philemon Dickenson.

On a joint expedition under Lieutenant Rhind, the USS Crusader and Planter carried troops to Simmons Bluff, Wadmelaw River, South Carolina, where they destroyed a Confederate encampment.

The Southern steamer had been designed to use only wood as fuel, a scarce commodity for the Union blockaders off Charleston, South Carolina.

In the fall of 1862, Du Pont ordered her transferred to the Union Army for service near Fort Pulaski on the coast of Georgia.