Archaeological evidence of past human activity in the region is abundant. Signs of habitation during the Neolithic Period [6,000 – 2,600BC] have been revealed at a number of locations including the caves of Ideon Andron on Mt. Ida (Psilorites), Gerani on the coast a few kilometers west of Rethymnon and Elenon in the district of Amari. During the Minoan Period [2,600 – 1,100BC] there seems to have been a great expansion of the population, throughout the region with habitation developing beyond the original cave dwellings into more organised social structures.
The Early Minoan Period [2,600 – 2,000BC] is best represented in the Rethymnon Prefecture at the sites of Chamalevri and Apodoulou in the Amari district; while the Mylopotamos area has the Sentoni cave near Zoniana, Pyrgi and Eleftherna. The Middle Minoan Period [2,000 – 1,600BC] brought developments such as the ‘palace’ constructions of Monastiraki in the Amari district, settlements at Pera Galinous in the Mylopotamos area and Stavromenos; alongside evidence at the caves of Melidoni and Patsos in the Rethymnon Prefecture. Important evidence of social structures and developments during the Late Minoan Period [1,600 – 1,100BC] can be seen at the settlement of Zominthos near Anogia, the religious site of Fantaxospilisra in the village of Prinos and the famous necropolis (cemetery) at Armeni.
The Geometric and Daedalic (7C) Periods [1,100 – 620BC] witnessed the flowering of important cities including Eleftherna and Axos (Oaxos), and the contemporary settlement at Mt Vrysina on the Onythe plateau. This continued apace through the Archaic Period [620 – 500BC] which saw the production of important great works of art in the region. The Classical [500 -330BC] and Hellenistic [330 – 67BC] saw the development of the ancient city of Rithimna possibly located within the bounds of modern Rethymnon. Other contemporary cities of the region, such as Eleftherna, Axos, Lappa and Syvritos retained their importance into the Graeco-Roman Period [67BC – AD323].
The First Byzantine Period [330 – 823] saw the transfer to Byzantium of status as capital of the Roman Empire and it’s renaming as Constantinople (326). Crete was then a part of the Eastern Empire, being governed by a Byzantine general. From this time Christianity flourished on Crete and, in the 8th century, the Episcopate of Crete was integrated into the Patriarchate of Constantinople. During this early Christian and First Byzantine period many churches were built on the island, the remains of some of which can still be seen. During the period 824 – 961 Crete was under Arab rule. However, in the Rethymnon region, little material archaeological evidence of this time is known. One exception to this is a find of Arab coins from the village of Giannoudi.
In the Second Byzantine Period [961 – 1210] the first fortification of Rethymnon was begun. Subsequently, the year 1211 saw the beginning of the important period of Venetian rule [officially 1204 – 1669].