The North Carolina Squadron was formed in 1861 prior to North Carolina’s secession from the United States. Marshall Parks (of the Albemarle and Chesapeake Canal Company) was appointed as commissioner along with Commander William T. Muse to establish a North Carolina Navy by the Governor and Council of North Carolina.

The side-wheeler Winslow, purchased in Norfolk by the authorization of Governor Ellis, was the North Carolina navy’s first ship. She began operating as a privateer out of Hatteras Inlet under the command of Lt. Thomas M. Crossan . Three small screw propeller canal tugboats were purchased and outfitted as gunboats at Gosport Navy Yard in early 1861 as well: the Beaufort, Raleigh, and Ellis.

After North Carolina seceded on 20 May 1861, the four vessels of the North Carolina Navy were turned over to the Confederate States government. On 22 June 1861, Flag Officer Samuel Barron took command of the naval defenses of North Carolina and Virginia. Commander Arthur Sinclair commanded the Winslow at this time; Commander W. B. Muse, the Ellis; Lt. Commanding J. W. Alexander, the Raleigh; and the Beaufort was commander-less. Lt. R. C. Duvall and his crew left her tied up to the dock in New Bern and formed an artillery company when he was refused a commission in the C.S. Navy. Lt. Commanding William H. Parker was assigned to command the Beaufort.

Two side-wheel steamers (the Sea Bird and Curlew) and two more canal tugboats (the Empire and Edwards) joined the squadron by the end of the summer of 1861. The Empire was later renamed the Appomattox; the Edwards became the Forrest. The Junaluska, another canal tugboat, saw service with the North Carolina Squadron during the fall of 1861, transporting troops and participating in the capture of the USS Fanny on 1 Oct 1862. The wooden schooner M. C. Etheridge (renamed the Black Warrior) was pressed into service at the battles of Roanoke Island and Elizabeth City.

Flag Officer Barron assumed command of Fort Hatteras on the second day of the Union fleet’s attack at Hatteras Inlet and was subsequently captured along with most of the garrison. The Ellis and the Winslow assisted in the evacuation of those that escaped. Flag Officer William F. Lynch replaced Barron as commander of the North Carolina Squadron on 4 September 1861. Lynch commanded the “mosquito fleet” during the battles of Roanoke Island and Elizabeth City.

The Winslow struck a sunken wreck at Ocracoke Inlet in November of 1861 and sank. The Curlew sank during the battle of Roanoke Island on 8 Feb 1862; the rest of the squadron retired to Elizabeth City once they exhausted their ammunition. Under the command of Commander S. C. Rowan, fourteen Union ships pursued the North Carolina Squadron up the Pasquotank River.

Rowan’s gunboats destroyed most of the “mosquito fleet” in a battle at Elizabeth City on 10 Feb 1862. The Black Warrior was set afire by her crew and abandoned during the battle. A shell from the Commodore Perry pierced the Fanny; she was run aground and set on fire near Fort Cobb. The Commodore Perry rammed and sank the Sea Bird as well. A boarding party from the Ceres captured the Ellis by hand-to-hand combat. The Forrest, disabled in the battle of Roanoke Island, was on the ways undergoing repairs; she was burned to prevent her from falling into Union hands, as were two boats under construction. The Appomattox escaped upriver after her gun was accidentally spiked, but her crew destroyed her when she was found to be two inches too wide to fit through the locks of the Dismal Swamp Canal.

Of the “mosquito fleet”, only the Beaufort and the Raleigh remained after the battle at Elizabeth City. The Raleigh had been dispatched to Norfolk on 9 Feb 1862 in search of ammunition and had not yet returned at the time of the battle. Lynch ordered the Beaufort’s crew ashore during the battle to man the four-gun battery at Fort Cobb; Lt. Commanding Parker sent the Beaufort up the river to Norfolk to prevent her capture. The Beaufort and Raleigh served as tenders to the Virginia in the battle of Hampton Roads. They were later transferred to the James River Squadron.