On the night of 31 January, CSS Palmetto State and Chicora, both Confederate ironclad rams, slipped out of the main ship channel of the harbor.

They hoped to recapture British iron propeller Princess Royal, taken by Union blockaders two days earlier with two powerful steam engines for new Confederate ironclads aboard.

Mercedita was the first Union ship the southern raiders encountered, and Palmetto State succeeded in ramming her, ripping a hole in her keel, piercing her boiler, and leaving her in a sinking condition.

However, the Confederate rams – eager for further action – accepted paroles for Mercedita's officers and crew and sped off to attack Keystone State, Quaker City and Augusta before retiring to Charleston.

It was my part, on the memorable morning, to aim and fire one effective shell into the Keystone State while running down to attack us, which (according to Captain LeRoy’s report), killing twenty-one men and severely wounding fifteen, caused him to haul down his flag in token of surrender.

In April, she was attached to the West Indies Squadron, to escort California steamers over part of their route, from New York to Aspinwall, Panama.

Arriving at Ciudad de Santo Domingo on 11 August, the ship found the country in an unsettled political state, but there was no sign of the reported Spanish man-of-war on the southern coast.