At the beginning of the Civil War, Cedar Key was an important transportation center as a Gulf port city, and as the western terminus of the Florida Railroad from Fernandina. During the war, the Cedar Keys area was an active center for blockade running and salt production.

In January 1862, a Union landing party from the USS Hatteras entered the town and destroyed the railroad depot and other buildings, the railroad wharf, railroad cars, several vessels, and the abandoned Confederate defenses.

Most of the Confederate troops stationed at Cedar Key had been sent to Fernandina just days before in anticipation of a Union attack there. A small force of 23 men from the 4th Florida Infantry was left to defend the town, and 15 of them were taken prisoner while attempting to flee in a ferryboat; the remainder escaped.

The town was blockaded by Union naval vessels of the East Gulf Blockading Squadron for the next two years. By 1864, Union forces had established a permanent military presence in the town and it became a base for conducting raids into the interior. During a return from one such raid in February 1865, a Union force of nearly 400 men from the 2nd U.S. Colored Infantry and the 2nd Florida Union Cavalry under the command of Major Edmund C. Weeks was attacked by a Confederate force of 145 men from several Florida units commanded by Captain J.J. Dickison at Station Four on the outskirts of Cedar Key.

After a daylong fight, the Union force withdrew back into Cedar Key. Casualty reports differed, with Major Weeks reporting that he had lost 5 killed, 18 wounded and 3 taken prisoner and that the Confederates suffered at least 2 dead, while Captain Dickison reported total Union casualties of 70 and Confederate losses of just 5 men wounded.

Information Provided by the Florida Department of State.