The first habitation in the area of Palaiochora (Amnissos) dates back in the Middle Minoan period (19th century B.C.).

The site is mentioned as a-mi-mi-so in the Linear B tablets. The Minoan "Villa of the Lilies" was destroyed by fire in the 15th century B.C. but complexes C and E continued to be inhabited until the 12th century B.C. In the Archaic period (7th century B.C.) the sanctuary of “Zeus Thenatas” was founded and remained in use until the 2nd century A.D. After a long period of abandonment, the hill was inhabited again during the Venetian occupation. 

Consolidation works and clearing are carried out at intervals by the 23rd Ephorate at the "Villa of the Lilies" and the sanctuary of Zeus.