Agios Nicolaos contrary to the other urban centers of Crete was not always an important settlement. In the Minoan years there was a small harbor, a little northern than the current one. On the hill between the lake of Agios Nikolaos and the current Marina, existed the ancient city of Lato that it appears to exist during the precocious Byzantine period.

Chania is one of the oldest cities in Greece. Where the current city of Chania now stands once lay the ancient city of Kydonia, which was one of the biggest towns during Minoan Crete. According to legend the town was built by Kydon grandson of Minoa. Accounts of the city were made throughout this period (geometrical progression, Archaic). Remarkable was her resistance against the Romans, but unfortunately the supreme Cointus Caicilus Metallus 69 BC had the powers to occupy the city. Kydonia was to continue flourishing throughout the Roman and Byzantine period and became the seat of the bishop; it was finally destroyed when raided by the Arabs around 824 AD.

During the Minoan period the centre of the region was Knossos. Heraklion was inhabited from the beginning of the first millennium BC. Quoted by Plinio as being a small city. Throughout the Minoan period it was one of the harbours for Knossos (Heraklia). The Venetians built the settlement and called it Kastro (castle). The Arabs selected Heraklion to be the capital of Crete as it had a well fortified harbour which they used as an operations base for their raids in the Aegean. It was to remain the capital until 1851 and then again from 1971. The Arabs called her fortress Tafrou (trench/moat) in Arabic Hantiak which is were the name for the town Handakas originated and it kept this name until the 19th century.

The first archaeological findings of civilization in the area are from the late Minoan period. Its ancient name was Rethymna.The area developed during the 5th and 4th century BC but towards the end of the Roman period the town began to decline. It flourished again during the Venetian rule when it became an important export centre and seat Lektor (today’s prefecture). Also their knowledge in letters and art grew, here was founded the Academy VIVI (1562 with the initiative of Francesco Barrozi), first intellectual association in Greece and one of the first in the whole of Eastern Europe. During this period of Venetian rule the city underwent repeated revolts from the Cretans.