USS Two Sisters was a small 54-ton captured Confederate schooner acquired by the Union Navy from the prize court during the American Civil War.

Two Sisters was put into service as a gunboat and, when required, as a ship's tender, by the Union Navy to patrol navigable waterways of the Confederacy to prevent the South from trading with other countries.

Two Sisters continued her patrols on the blockade through the spring, summer, and early fall, keeping a wary eye on the route between Bayport, Florida, and Havana, Cuba.

On 13 January 1864, while Two Sisters was stationed off the mouth of the Suwannee River, a boat crew debarked from her and captured the schooner William with its cargo of salt, bagging, and rope.

The Union schooner's patrol duty was broken in May by service as tender to the steam frigate USS San Jacinto.