In the fall of 1861, Drayton was placed in command of the gunboat ; he participated in the capture of Port Royal, South Carolina. His older brother Thomas F. Drayton, a graduate of West Point and classmate of Jefferson Davis, had resigned with the secession of South Carolina. He was a general of the Confederate army and commanded the forts destroyed in this engagement. The Union forces captured Hilton Head, Beaufort and Parris Island and used them as a base to continue operations against Savannah, Georgia and Charleston, South Carolina.