The first signs of man on La Maddalena date back to the prehistoric period, as confirmed by traces found on the peninsula of Abbatoggia, in the north-west of the island. The remains in the area between the bays of Cala Gavetta and Cala Chiesa in the south are evidence of a Roman settlement dating back to the period between the first half of the 1st century BC and the 4th century AD.
The site continued to be occupied until the Middle Ages, when the island was called Porcaria and was particularly well-known for the monastery “de Sancto Angelo de Porcaria”, belonging to the Benedictine order.
Subsequently, La Maddalena remained uninhabited, or nearly, for several centuries. The inhabitants returned during the 18th century and the current town was founded in 1777 at Cala Gavetta. The town developed quickly and was given a system of fortifications where war ships landed. In 1804, Admiral Horatio Nelson established his logistics base for his fleet in the Mediterranean and stayed there for about three years before the Battle of Trafalgar. When in 1943, after the fall of Fascism, the king had Mussolini arrested, the dictator was taken there and held prisoner. He spent some time at Villa Weber before being transferred to the Gran Sasso.
The ancient settlements on the island of Caprera date back to the Imperial Roman era. They were concentrated around the western coastal areas close to the islands of La Maddalena and Santo Stefano. Traces of a garrison of this period have been identified at Arcaccius along the central western shores. Some necropoli have been discovered in the hinterland of Cala Scavicco, in the Tola valley and in Petrajaccio, in the south west of the island.
In 1767, together with other islands in the archipelago, it was occupied by the Sardinian navy and annexed to the kingdom. In 1854, Giuseppe Garibaldi settled there and built a house, which he turned into a farm. He left in 1859 to take part in the War of Independence and the Expedition of the Thousand. He returned in 1867 and remained there until his death in 1882.
The three islands of Razzoli, Budelli and Santa Maria constituted the dismantling between 3000 and 2000 BC of a united island complex that had formed during the Flandrian Transgression of 6000 – 3000 BC. The use of the narrow straits between the islands by the ancient navy is suggested by the discovery if a fragment of an Attic kylix, dating back to the mid 5th century BC. The only one of the three islands that was certainly inhabited in ancient times was the Island of Santa Maria, where there is evidence of the 13th century Ecclesia Sancte Marie de Budello.
The island of Santo Stefano is roughly rectangular in shape and its coastline has a single cove, Cala Villamarina, where archaeological excavations have confirmed a mid Neolithic settlement.