Native Americans associated with Timucan mound-building culture settled on Amelia Island about 1000. They called the Island Napoyca. They would remain on Naypoca until the early 1700s.
The history of fernandina on Amelia Island has unfolded under eight flags. The French flag was the first to fly over the island. Jean Ribault, French explorer, landed in 1562. He named the island Isle de Mar. Spanish forces led by Pedro Menendez de drove out the French in 1565. They killed Ribault and 350 French colonists.
The Spanish flag was the second flag. in 1573, Spanish Franciscans established the Santa Mraia mission on the Island. They renamed the island Isla de Maria. Fernandina was settled in 1685. It was located in the area now called "old town." British faders destroyed the town in 1702. The area was deserted for many years.
James Oglethorpe, the founder of Georgia, scouted the area. He found peach trees, orange groves, and deserted fields. He renamed the island "Ameilia island" in honor of princess Amelia, the daughter of King George II of England. Florida and Fernandina came under British rule. The English flag was raised as the third flag in 1763.
In 1783, Spain again controlled Florida. A land grant became a plantation on the site of present-day Fernandina. The patriots of Amelia Island attempted to transfer Ameilia Island to the control of the United States. Their plan failed and Spain regained control.
1817, Sir Gregor MacGergor and 55 men captured the Island from Spain. They raised their own green cross of Florida flag which became the fifth flag.
The same year, pirate Luis Aruy sailed with his armada of three ships into the harbor. Three days later he hoisted the republic of Mexico flag, the sixth flag. Fernandina became a pirate haven and location for buried treasure.
In 1821, the United states took control. the American flag, the seventh flag, was raised. The building of Fort clinch begun. U.S. Senator David yulee built Florida's first cross-state railroad.
The confederate flag, the eighth flag to fly over Fernandina, appeared with the outbreak of the civil war in 1861.