The continuous habitation and the numerous physical and human catastrophes destroyed almost without a trace the ancient city of Heraklion, which was mentioned by Strabo as a port of Cnossos. The small natural harbor and the sandy haven were probably exploited as soon as the Minoan period, since scatter findings from the Minoan to the Roman period have come to light. During the Hellenistic period the city received mighty fortification walls and had a significant extent. During the roman period it was considered to be one of the few well-protected harbors of the northern coast of the island (Stadiasmus Maris Magni). A luxurious roman villa with mosaic floors, burials with lavish offerings, scattered sculptures, a huge column capital in its second use and several inscriptions testify the wealth of the city during the Roman period. In the Early-Byzantine period the city became a bishopric seat. In the Synodical catalogues it was mentioned either as Heracleae (343 A.D.) or later as Herakleioupolis (7^th Ecumenical Synod).

Excavations have brought to light a vast amount of findings (architectural sculpture, pottery, coins and small findings), but only a few relics of constructions. From the middle of the 7^th c. (654 A.D.) the city begun to feel threatened by the presence of the Arabs in the Aegean Sea. In order to prevent a catastrophe, the Byzantines decided to fortify the city with new walls, using blocks from the Hellenistic enceinte, just like they did in other important settlements around the island. Nevertheless, the sturdy enceinte, its quadrangular defensive towers and the moat, which led the Arabs to name the city Rabdh el Khandaq (The Fortress of the Moat), were proved ineffective. The Arabs debarked on the island from the South, probably the area of Keratokambos, and gradually conquered it until 828. For the next 150 years, Heraklion, which was the last to fall, became the base of the Arabic raids and trade around the Mediterranean. A large amount of Arabic bronze coins and pottery of high quality, imported both from the East and the West (Spain), testify the long lasting presence of the Arabs in the city, which left its indelible mark to its name; Khandaq (moat, trench) became Chandax for the Byzantines and Candia for the Venetians.

The loss of Crete was a severe strike to the Byzantine predominance on the Mediterranean. Its recapture though was even harder. After a series of wasted efforts, in 961 the Byzantine general of the army, and later an emperor, Nicephoros Phocas, managed to recapture the city, by mining its walls. The city gradually gained back its wealth and up to the end of the 12^th c. knew a significant commercial and economic development. Nevertheless, just before the Fall of Constantinople to the Franks in 1204, the deposed Byzantine emperor Isaac II offered the island of Crete to Boniface of Montferrat as a reward for helping him regain the throne. Boniface in his turn sold the island to the Venetians. After a short capture by the Genoese Enrico Pescatore and his pirates, in 1211 the city came under the rule of Venice. Candia became the capital of the Venetian Kingdom of Crete, the most important trade station of Venice in the Eastern Mediterranean, a place where literature and fine arts flourished for many centuries.

When Cyprus fell to the Ottomans in 1571, Candia became the sole military base of Venice in the East Mediterranean. The Venetians tried to protect it with a new, huge enceinte, which gave the city its latest name: “Megalo Kastro” (The Large Fortress). But after 21 years of fierce siege and resistance, which is known as “the Cretan War”, in 1669 the last defender of the city Francesco Morosini was forced to surrender it to the forces of the Sultan.