From the 14th century there was a fortress on the islet. The constructions started in 1573 by the Venetians, in an effort to reinforce the defense of the port. However, the constructions alone could not solve the problem of security. The military experts had requested complementary defense constructions in other crucial parts of the gulf, which were completed due mainly to high cost.
The architect and supervisor of the constructions was Latino Orsini. The works proceeded very fast and within a year, the first canons were placed. In the years that followed, until the Turkish invasion in 1645, conservation and other complementary works for the fortification’s improvement were taking place. During this time is dated the1585 construction and the central temple, which is well preserved until today. The temple hosted clergymen of the St. Augustine order, since an Augustinian monastery pre-existed on the islet. The Fortezza fortress was an example of excellent fortification work, taking advantage of the islet’s morphology. Its strategic construction provided smart solutions to possible threats from the mainland and the sea. In the interior, except from the areas of military use, there were also areas of public interest, numerous churches, a hospital, a prison, and underground water tanks. After the occupation of the city of Chania from the Turkish army in 1646, the Fortezza fortress was brutally attacked from the ground and the sea. However, the few armed defenders of fortress were able to save it. After the occupation of Handakas (today the city of Heraklion) in 1669, the islet remained under Venetian possession after negotiations and agreements. The islet remained in Venetian possession until September 27, 1715, when it was finally surrendered to the Turkish army after a long siege and heroic resistance that lasted for 72 days. The Turks occupied the islet until 1898 when the Turkish forces departed from Crete. During the period of Turkish occupation on the islet, no major changes or addition were made in the fortress, except the transformation of the central temple to a mosque, dedicated to Sultan Gazi Ahmet Han.
The islet of Souda is connected with the Cretan history and the battles of the Cretan people for freedom, as it played a crucial role during battles and became a refuge for the revolutionaries throughout the Turkish occupation, when the islet was in Venetian hands. On this islet, the Greek flag was raised for the very first time on February 1, 1913 (before the official unification of Crete with Greece). After World War 2, the islet is in the hands of the Greek forces, in the framework of a wider plan of defense of the port. In 1966, the Greek marine forces planted trees on the islet, where before there was a complete lack of plantation.