La Maddalena has undergone many name changes: the Romans named it Ilva, Fussa and Bucina and in the Middle Ages the island was known as "Bicinara" before being given the name of Santa Maria Magdalena in the 16th century. After this it finally became known as La Maddalena.
The Maddalena archipelago, is known from archaeological evidence to have been occupied in prehistoric times, but its written history begins with the Roman Empire.
With the fall of the Roman Empire the islands were completely abandoned until the 12th century, when he was chosen by Benedictine monks founded small communities there. The islands were the object of a dispute between the Republics of Pisa and Genoa in the 12th century.
In 1584 all the monasteries on the islands were destroyed by one of the Ottoman raids. In the XVII century shepherds began to bring their flocks to the islands in the winter months.
Its location in the Strait of Bonifacio, through which much maritime traffic must pass, has turned the archipelago into a strategic military position. In 1767 it was occupied by the Savoy-Piedmontese. The nucleus of the present town of La Maddalena emerged then.
In 1793 a French expedition, in which Napoleon Bonapart took part, unsucsessfully tried to occupy the island. It was the first combat experience of Napoleon Bonapart. During all the Napoleonic Wars Admiral Goratio Nelson used the archipelago of La Maddalena as a base for his fleet in actions against the French.
A base was established here by the Italian Regia Marina (Royal Navy) in 1887. In 1943, during World War II, Benito Mussolini was briefly held prisoner here.
From 1972 through 2008, there was a NATO base on the nearby island of Santo Stefano. The NATO base housed an Italian Navy barracks and it served as the home port for several US Navy submarine tenders over the years, ending with the departure of the USS Emory S. Land, which set sail for its new home port of Bremerton, Washington. The US Naval Base officially closed in January 2008, ending the 35 year US presence in La Maddalena.
During the period in which the American military had a presence on the island, the most noteworthy event happened on October 25, 2003 when submarine USS Hartford ran aground with sufficient force to substantially damage its rudders, sonar and electronics.
La Maddalena now lends its name to an Italian National Park located in the archipelago.