David Levy Yulee, one of the first United States senators from Florida, established the first cross-state railroad running from Fernandina Beach to Cedar Key, which opened on March 1, 1861.

The field work and scholarship of archeologists and historians in the last forty years has advanced understanding of the area's Native American history after European contact.

In later colonial times the site gained military importance because of its deep harbor and its strategic location near the northern boundary of Spanish Florida.

During his invasion of north Florida, 1736–1742, the governor of the British colony of Georgia, James Oglethorpe, stationed a military guard of Scottish Highlanders on the site and named the island after Princess Amelia, the daughter of King George II of Great Britain.

Oglethorpe withdrew his troops in 1742, and the area became a buffer zone between the English and Spanish colonies until the signing of the Treaty of Paris in 1763, when Spain traded Florida to Great Britain for control of Havana, Cuba.

The so-called "New Settlement" (present-day Old Town), on the south side of the mouth of Egan's Creek adjoining the Amelia River, was presumably its headquarters.

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

When Spain regained possession of Florida in 1783, the Amelia harbor served as an embarkation point for loyalists abandoning the colony who tore down the buildings and took the lumber with them.

In trade for the earlier British grant,[2] the Spanish authorities awarded her 150 acres within the present-day city limits of Fernandina Beach.

[13] On January 1, 1811, the town of Fernandina, which was about a mile from the present city, was named in honor of King Ferdinand VII of Spain by the governor of the Spanish province of East Florida, Enrique White.

On May 10, 1811,[14] White's successor and acting governor at the time, Juan José Estrada, instructed the newly appointed Surveyor General, George J. F. Clarke, to plat the township[15] in accordance with the 1542 Spanish Laws of the Indies (Leyes de Indias).

Because it was a center for smuggling and represented a threat to trade of the United States, Fernandina was invaded and seized by forces under the command of General George Mathews in 1812 with the clandestine approval of President James Madison.

[19] A group of Americans calling themselves the "Patriots of Amelia Island" had banded together to drive out the Spanish and reported to General Mathews, who moved into a house at St. Marys, Georgia, just nine miles[20] across Cumberland Sound.

[21] They were supported by slave-holding planters who wanted to stop raiding parties of Seminole Indians from the Alachua region and feared the presence of armed free black militias in Spanish Florida.

[24] On March 16, nine American gunboats under the command of Commodore Hugh Campbell formed a line in the harbor and aimed their guns at the town.

[25][26] General Mathews, still ensconced at Point Peter on the St. Marys in Georgia, ordered Colonel Lodowick Ashley to send a flag to Justo Lopez, commandant of the fort and Amelia Island, and demand his surrender.

The next day, a detachment of 250 regular United States troops were brought over from Point Peter, and the newly constituted Patriot government surrendered the town to General Matthews, who had the stars and stripes of the U.S. flag raised immediately.

A Scottish military adventurer and mercenary, Gregor MacGregor, claimed to be commissioned by representatives of the revolting South American countries to liberate Florida from Spanish rule.

[30] Financed by American backers,[31] he led an army of only 150 men including recruits from Charleston and Savannah, some War of 1812 veterans, and 55 musketeers in an assault on Fort San Carlos.

Now in possession of the town, and seeing the need to make the appearance of a legitimate government, MacGregor quickly formed a committee to draft a constitution,[36] and appointed Ruggles Hubbard, the former high sheriff of New York City, as unofficial civil governor, and Jared Irwin, an adventurer and former Pennsylvania Congressman, as his treasurer.

MacGregor then opened a post office, ordered a printing press to publish a newspaper, and issued currency to pay his troops and to settle government debts.

[37][38] Expecting reinforcements for a raid against the Castillo de San Marcos in St. Augustine,[39] MacGregor intended to subdue all of Spanish East Florida.

[48] When about August 28 fellow conspirator Ruggles Hubbard sailed into the harbor aboard his own brig Morgiana, flying the flag of Buenos Ayres, but without the needed men, guns, and money, MacGregor announced his departure.

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

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

[50][51] Before he left Florida, MacGregor had met with the French privateer, Louis Aury, a previous acquaintance from political intrigues in South America who had served with him in Simon Bolívar's army in New Granada.

Realizing they had nothing to gain by opposing him, a compromise was reached and they made an alliance with the Frenchman:[56] Aury would be commander-in-chief of military and naval forces, Irwin his adjutant general, and Hubbard the civil governor of Amelia.

His company began construction in 1855, and the original site of Fernandina, the one-time smugglers' den and freebooter haven, lapsed into quiet obscurity.