Knowing that the Spanish had claimed the area in 1513 did not prevent these French colonists from landing as not only were they seeking land for France but also refuge from the religious and political persecution that went along with being Huguenots. Though Ribault and his company didn't remain, the Huguenots returned again in 1564 under the leadership of René de Laudonniere who was also a commander on the first voyage. The second colony constructed Fort Caroline in Northern Jacksonville near the mouth of the St. John's River. Things were short lived however, because in 1565, Spanish troops led by Pedro Menéndez de Aviles brutally slaughtered these French settlers in order to regain the territory they had plotted as their own years prior.

The first Spanish reign was from 1565 to 1763 and they set up the mission of  Santa Maria on the northern end of Amelia Island in what is now known as Old Town in order to convert the Indians to Christianity. In fact the island became known as "Isla de Santa Maria." From this point on the Timucuan numbers started to decline because of the influx of European disease and the stresses due to the disruption of their lifestyle. Though their numbers were once about 30,000 they were almost completely extinct within about 100 years of their first contact with the Europeans.

The British settlements in the North soon took a keen interest in the area because of the naturally deep ports and the strategic trade route location. The island was named Amelia by Georgia's governor James Oglethorpe in 1735 in honor of Princess Amelia, daughter of King George II.  Though the Island was named Amelia by the British, it did not fall into British hands until Spanish Florida was traded for British Cuba in 1763 as a result of the Treaty of Paris. During the time of British rule which lasted until 1783, the island was known as Egmont. 

In 1783, the Second Treaty of Paris ends the Revolutionary War and returns Florida to Spain. British inhabitants of Florida had to leave the province within 18 months unless they swore allegiance to Spain. In 1811, surveyor George J. F. Clarke plats the town of Fernandina, named in honor of King Ferdinand VII of Spain. 

To drive out the Spanish, the "Patriots of Amelia Island," an independent group of American civilians backed by the United States government, seized control of the island and raised their flag on March 17, 1812. The next day, they "ceded" Amelia Island to the United States. However, Spain’s strong protest forced the U.S. to relinquish its new possession, especially in light of the impending War of 1812 with England.

A Scottishman named Sir Gregor MacGregor with the support of some key Americans ran the Spanish off the island in 1817 and later raised the "Green Cross of Florida" flag. However, because of lack of reinforcements and funds he left and his lieutenants became in charge. They made a deal with Frenchman Luis Aury (a soldier in the Mexican Revolution) in order to get support to maintain their control. However, Aury, in return for giving them support wanted to command the island and so raised the Mexican flag. The town came into such a state of bedlam that the U.S. government sent gunboats and took control and held Amelia Island in trust for Spain until Florida became a U.S. territory on July 10, 1821.

The Confederates took control of Fort Clinch which had been started by the Federals and later abandoned because of the outbreak of the Civil War. The "stars and bars" of the Confederate flag were raised at Fort Clinch in April 1861. General Robert E. Lee visited the fort two times during this period. Less than a year later Union forces surrounded the fort with 28 gunboats and Union control held throughout the remainder of the war.

In the golden age of the island from about 1870 to 1910, many wealthy Americans made Fernandina their home and built elegant Victiorian style homes in what became known as the Silk Stocking District. The boom was due to the shipping industry and the fact that many New Yorkers were coming down by steam boat to enjoy the warm climate and elegant hotels. The Egmont Hotel which was one of the grandest hotels of the times was even visited by Ulysses Grant. 

In 1890 Standard Oil co-founder Henry Flagler opened up the railroads and this detoured much of the tourist traffic to St. Augustine and places farther south. Flagler's actions resulted in a faltering local economy until some American and immigrant fishermen saw the potential in the area for the shrimping industy which was thus given birth here in the early 1900s. Following this, two mills were located here which provided an additional boost to the economy and also created many local jobs.

In modern times the Amelia Island Plantation was built as a resort with a natural setting in the 1970s which caused the area to become solidly placed on the map as a tourist and resort area. In more recent years the Ritz-Cartlton Amelia and a number of other facilities have been built  furthering the reputation of the area for fine amenities, conventions, golfing, and many other activities. 

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