The pre-Columbian era was marked by regular, routine, and possibly minor tribal wars with neighbours. Timucua is organized into as many as 35 chiefdoms, each of which has hundreds of people in various villages within its scope. They sometimes form loose political alliances but do not operate as a single political unit.
An archaeological dig at St. Augustine in 2006 uncovered a Timucuan site dating to between AD 1100 and 1300, predating the city's founding by Europeans by more than two centuries. Included in the find were pottery, with pieces from the Macon area, Georgia, indicating a vast trading network, and two human skeletons. This is the oldest archaeological site in the city.
The Timucua were probably the first Native Americans to see Juan Ponce de León's landing near St. Augustine in 1513. This idea is disputed as most historians now agree that Ponce de León's landing point was likely to be further south in the Ais Territory, near Melbourne Beach. If so, Timucuan contact with that particular expedition is unlikely. Later, in 1528, Pánfilo de Narváez's expedition passed through the western fringes of the Timucua region.
In 1539, Hernando de Soto led an army of over 500 men through the western part of the Timucua region, stopping at a series of Ocale, Potano, North Utina, and Yustaga branch villages in Timucua on his way to the Apalachee domain (see list of sites and peoples visited by Hernando de Soto Expeditions for other sites visited by de Soto).
His troops confiscated food stored in villages, forced women into concubines, and forced men and boys to serve as guides and carriers. The army fought two skirmishes with the Timucua group, which resulted in heavy casualties in Timucua. After defeating the resisting Timucuan warriors, Hernando de Soto executed 200 people, known as the Napituca Massacre.
The first significant massacre by Europeans on what was then US soil (Florida). De Soto was in a hurry to reach the Apalachee domain, where he hoped to find enough gold and food to support his army for the winter so he did not linger in the Timucua area.
The Acuera were one of the few Native American groups to defeat the Spanish in battle in the early part of the de Soto entrada. However, this is likely due to the fact that the full forces accompanying the Soto were not sent against Acuera as well. as a relatively faster expeditionary journey during this period.
In 1564, French Huguenots led by René Goulaine de Laudonnière established Fort Caroline in present-day Jacksonville. They attempted to establish a further settlement along the St. Lawrence River. After the initial conflict, the Huguenots developed friendly relations with the local indigenous population of the area, especially with Timucua under the cacique Saturiwa.
A sketch of Timucua drawn by Jacques le Moyne de Morgues, a French settler, has proved to be a valuable resource for modern ethnographers in understanding the community. The following year the Spanish under Pedro Menéndez de Avilés surprised the Huguenots and ransacked Fort Caroline, killing all but 50 women and children and 26 who fled.
The other French had been shipwrecked off the coast and picked up by the Spanish, who executed all but 20 of them; this ended French settlement in Florida. This event caused a rift between the natives and the Spanish, though Spanish missionaries soon left.
The history of Timucua changed after the Spanish founded St. Augustine in 1565 as the capital of their Florida province. From here, Spanish missionaries established missions in every major town of the Timucuan principality, including the mission of Santa Isabel de Utinahica in what is now southern Georgia, for Utinahica. By 1595, the Timucuan population had dwindled by 75%, mainly from epidemics of new infectious diseases introduced through contact with Europeans and war.
In 1700, the population of Timucuan was reduced to only 1,000. In 1703, Governor James Moore led an army of colonists from the Carolinas with Creek, Catawba, and Yuchi allies and launched a slave raid against Timucua, killing and enslaving hundreds of them.
The 1711 census found 142 speakers of the Timucua language living in four villages under Spanish protection. Another census in 1717 found 256 people in three villages where Timucua was the majority language, although there were several residents with a different native language.
The population of the village of Timucua was 167 in 1726. In 1759, Timucua, under Spanish protection and control, numbered only six Timucua adults and five and a half children.
In 1763, Spain ceded Florida to Great Britain and brought less than 100 Timucua and other native people to Cuba. Research is being carried out in Cuba to determine if Timucua descendants are there. Some historians believe a small group of Timucua may have remained in Florida or Georgia and may have assimilated into other groups, such as the Seminoles.
Many Timucua artefacts are housed in the Florida Museum of Natural History at the University of Florida and other museums.