According to archaeological discoveries, man first arrived in the area in the later Neolithic years (3500-2800 BC). At present, Rethymnon is built on the site of ancient Rithymna, as the finds of a cemetery of the Late Minoan period, discovered in the Mastaba quarter, show. Minoan period (2800-1100 BC)Settlements and large building complexes (Elenes, Monastiraki, Apodoulou) appeared which were later flattened by earthquakes culminating in their final destruction in the earthquake of 1450 BC. This destruction was taken advantage of by the Mykenes who invaded and settled in Crete.
There is evidence of civilisation in the area of Eleftherna and its eastern areas including at least IS cities founded between 710 and 470 BC, the majority of which are small towns. Classical period (470-323 BC) Sivritos boomed as did Rithymna, the predecessor of today's Rethymnon.
During this period "Lappa" appears as the most important city. The 5th, 6th and first half of the 7th centuries AD were peaceful under the jurisdiction of the Byzantine Empire. Since the second half of the 7th century continuous Arab invasions disrupted Crete until it was finally conquered in 827 or 828. The successive attempts of the Byzantine resulted in its re conquest only one and a half century later (961 AD).
When the capital of the Roman Empire was transferred to the Byzantium and Constantinople was founded in 330, Crete was included in the East Roman Empire, constituting a separate district, which was governed by a Byzantine general. During the early Christian and First Byzantine period (330-824) a large number of temples were built, archaeologists have discovered many of which. Starting from the year 824 up until 961, the island was governed by the Arabs, although very little evidence of this fact was found in the area of Rethymno apart from some Arabian coins, which were found in the village of Giannoudi.
During the Second Byzantine period (961-1210) fortification works of the town of Rethymno were started for the first time as we shall see further on. In the year 1211 the long and interesting period of the Venetian occupation began, remains of which can clearly be seen still on all levels in the area of the town of Rethymno.Rethymnon became a city during the Venetian occupation. The Venetians needed an intermediary port for their operations for their ships travelling from Iraklion to Hania. They also needed a administrative center, so Rethymnon became the third bigger city in Crete and an important cultural center.
In its capacity as the most important centre in the region, it became the seat of the "Rettore" - the Venetian governor.Rethymnon suffered raids, fires and plunder by the terrible Khair-ed-Din Barbarossa and other pirates, and was finally taken by the Turks in 1646.The Turkish occupation brought with it a dark period for Rethymnon. The economy became agricultural, education ceased for a few centuries and oppression became unbearable. The Revolution at Sfakia in 1770 prepared for the uprising of 1821. It was in this revolution that the Arkadi Monastery near Rethymnon became world famous after the martyrdom of its defenders.
Crete was eventually unified with the rest of Greece in 1913 and since then it has followed the nation's history. In May 1941, Rethymnon was one of the German Parachutists' three fronts. The memorable resistance of the local people led to the execution of hundreds of inhabitants and the levelling of whole villages.