The island was named for Princess Amelia, daughter of George II of Great Britain,[2] and changed hands between colonial powers a number of times.

It is claimed that eight flags have flown over Amelia Island: French, Spanish, British, Floridian/Patriot, Green Cross, Mexican, Confederate, and United States.

[5] In 1562, French Huguenot explorer Jean Ribault became the first recorded European visitor to Napoyca, and he named the island Île de Mai.

[14] In 1702, the Spanish abandoned these missions after South Carolina's colonial governor James Moore led an invasion of Florida with British colonists and their Native American allies.

The area became a buffer zone between the English and Spanish colonies until the Treaty of Paris (1763) settling the Seven Years' War, in which Britain defeated France.

Its headquarters were presumably the so-called "New Settlement" on the south side of the mouth of Egan's Creek adjoining the Amelia River, the site of the present-day Old Town.

[24] In the late 1770s and early 1780s, during the American Revolutionary War, British loyalists fleeing Charleston and Savannah hastily erected new buildings at the settlement, calling their impromptu town Hillsborough.

In June 1785, former British governor Patrick Tonyn moved his command to Hillsborough town, from which he sailed to England and evacuated troops and Loyalists later that year.

In trade for the earlier British grant,[27] the Spanish authorities awarded her 150 acres (61 ha) within the present-day city limits of Fernandina Beach.

Colonel Charles Howard, an officer in the Spanish military, discovered that the rebels had built a battery and were flying the French flag.

[32] General Mathews moved into a house at St. Marys, Georgia, just nine miles[31] across Cumberland Sound from Fernandina on the northwest end of the island.

From Point Peter, General Mathews ordered Colonel Lodowick Ashley to send a flag to Don Justo Lopez,[33] commandant of the fort and Amelia Island, and demand his surrender.

The next day, March 17, a detachment of 250 regular United States troops were brought from Point Peter, and the newly constituted Patriot government surrendered the town to General Matthews.

Gregor MacGregor, a Scottish-born soldier of fortune, led an army of 150 men, including recruits from Charleston and Savannah, some War of 1812 veterans, and 55 musketeers, in an assault of Fort San Carlos on June 29, 1817.

[39] On September 4, faced with the threat of Spanish reprisal, and lacking money and adequate reinforcements, MacGregor abandoned his plans to conquer Florida and departed Fernandina for the Bahamas with most of his officers, leaving a small detachment of men at Fort San Carlos.

[40] The garrison and a force of American irregulars, organized by Ruggles Hubbard and former Pennsylvania congressman Jared Irwin, repelled the Spanish attempt to reassert authority.

On September 13 the Battle of Amelia Island started when the Spaniards erected a battery of four brass cannons on McLure's Hill east of the fort.

[40][41] Hubbard and Irwin later joined forces with French-born pirate Louis-Michel Aury, who laid claim to Amelia Island supposedly on behalf of the revolutionary Republic of Mexico.

He had formerly been associated with MacGregor in South American filibuster adventures,[42] Aury had also been a leader among a group of buccaneers based on Galveston Island, Texas.

[47] He directed his secretaries Pedro Gual and Vicente Pazos to draw up a constitution,[48] and invited all of Florida to unite in throwing off the Spanish yoke.

He stayed on the island more than two months as an unwelcome guest; Bankhead occupied Fernandina and President James Monroe vowed to hold it "in trust for Spain".

In the days before the American Civil War, Confederate sympathizers calling themselves the Third Regiment of Florida Volunteers took control of Fort Clinch on January 8, 1861.

In 1862 Secretary of War Edward M. Stanton had appealed to northern abolitionists for aid in caring for the thousands of freedmen who camped near Union forces in areas of South Carolina and Florida.