When communication was cut off with Washington at the start of the Civil War, Du Pont took the initiative of sending a fleet to the Chesapeake Bay to protect the landing of Union troops at Annapolis, Maryland. In June 1861 he was made president of a board in Washington formed to develop a plan of naval operations against the Confederacy. He was appointed flag officer serving aboard the steam frigate as commander of the South Atlantic Blockading Squadron, leading from Norfolk, Virginia, the largest fleet ever commanded by an American officer at that time. On November 7, Du Pont led a successful attack on the fortifications at Port Royal harbor in South Carolina. This victory enabled Union naval forces to secure the southern waters of Georgia and the entire eastern coast of Florida, and an effective blockade was established. On January 3, 1862, he was promoted to the newly created rank of Flag Officer (equivalent to the rank of Commodore, which would be created in July 1862). Du Pont received commendations from U.S. Congress for his brilliant tactical success, and was appointed rear admiral on July 16, 1862.