October 1: Democrat John Milton, a supporter of secession, was elected governor of Florida.
November 7: In the national presidential election, Republican Abraham Lincoln was elected. Democrat John C. Breckenridge received Florida's three electoral votes.
November 30: Governor Madison Perry (who would remain in office until the fall of 1861) signed into law a bill calling for a convention to meet in Tallahassee to discuss Florida’s secession from the United States.
December 22: Elections were held to send delegates to the Secession Convention.
January 3: The Secession Convention convened in Tallahassee.
January 10 : The Secession Convention voted 62-7 to adopt an Ordinance of Secession and withdraw Florida from the United States.
February 4: Representatives from Florida and six other Southern states met in Montgomery, Alabama to organize a new government.
February 22: The Confederate States of America was formally organized.
April 12 : Confederate bombardment began against Fort Sumter, South Carolina, marking the beginning of the Civil War. On the same day the First Florida Regiment arrived in Pensacola to try and drive the Northern troops out of Fort Pickens.
July 21: The first major battle of the war, a Confederate victory, was fought at Bull Run, or Manassas, Virginia. No Florida units were involved.
October 7: John Milton was inaugurated as Florida’s fifth governor.
October 9: Confederate troops landed on Santa Rosa Island to attack Union soldiers stationed outside Fort Pickens. After a sharp fight the Confederates were forced to retreat, suffering 87 casualties. The Federal losses totaled 62 killed, wounded, and missing.
November 22: A major bombardment occurred at Pensacola between Union-occupied Fort Pickens and surrounding Confederate batteries.
February – March: Due to defeats in Tennessee, most Confederate troops were withdrawn from Florida.
March 4: Northern troops occupied Fernandina.
March 11 – 12: St. Augustine and Jacksonville were occupied by Union troops. Jacksonville was occupied four different times during the war, while St. Augustine remained in Union hands for the rest of the war.
October 1 – 3: A Federal force landed on the St. Johns River below Jacksonville and forced the Confederates at St. Johns Bluff to abandon their positions.
January 1: President Lincoln formally issued his Emancipation Proclamation, which freed slaves in Confederate-controlled areas of the South. Although the Proclamation freed few slaves initially, it laid the framework for the Thirteenth Amendment, which would end all slavery in the United States.
May 27: The Confederate gunboat Chattahoochee exploded on the Apalachicola River, killing 16 sailors and wounding several others. The Chattahoochee helped guard the Apalachicola River basin, protecting that region from Union attack.
July 1 – 3: The Battle of Gettysburg, Pennsylvania was fought. Florida soldiers were heavily engaged in this Confederate defeat.
December 2 – 15: Union warships destroyed a large number of Confederate saltworks at Lake Ocala and West Bay. These saltworks, consisting primarily of large kettles for the boiling of seawater, were vital to the Confederacy. Salt was a precious commodity used in preserving food.
February 7: Union ships docked at Jacksonville, unloading a large number of troops who hoped to gain control over east Florida.
February 20: The Battle of Olustee was fought east of Lake City. It was the largest Civil War battle in Florida with over 5,000 men fighting on each side. The Confederates stopped the Union invasion of the interior, driving the Northern troops back to Jacksonville.
April 1: The Northern transport ship Maple Leaf was sunk by a Confederate mine in the St. Johns River.
September 27: Battle of Marianna, Florida. A small Confederate force of mainly old men and boys fought a bloody battle with a group of Union cavalry led by General Alexander Asboth. The Federals defeated the Confederates and burned part of the town.
February 21: A small Confederate force attacked Union-held Fort Myers, but was repulsed. The Battle of Fort Myers was perhaps the southernmost battle of the Civil War.
March 6: Union soldiers were defeated by the Confederates at the Battle of Natural Bridge. Among the Confederate defenders were old men and cadets from the West Florida Seminary (now Florida State University).
April 1: Governor John Milton committed suicide at his home near Marianna.
April 9: General Robert E. Lee surrendered his army of Northern Virginia (including a number of Florida soldiers) to Union General Ulysses S. Grant at Appomattox, Virginia.
April 14: John Wilkes Booth assassinated President Lincoln. Lewis Thornton Powell, alias Payne, the Florida native who was part of Booth's conspiracy to assassinate President Lincoln, Vice President Johnson and Secretary of State Seward, carried out his portion of the plot on the evening of April 14. Posing as a delivery man, Powell entered the home of Secretary of State William Seward and attacked the bedridden official with a knife inflicting serious but not fatal wounds.
April 26: Confederate General Joseph E. Johnston surrendered the last major Confederate Army near Durham Station, North Carolina.
May 10: Union General E. M. McCook accepted the formal surrender of Confederate troops at Tallahassee. During the remainder to the month smaller groups of Confederates surrendered throughout the state.