The first habitation in the area of Palaiochora (Amnissos) dates from 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 again inhabited during the Venetian occupation. The first excavations of the site were conducted at the villa by Spyridon Marinatos in 1929-1938. Parts of the "Mycenaean" settlement (LM III period) were later excavated by Stylianos Alexiou. In 1983-85 the buildings were cleared and drawn by the Archaeological Institute of the University of Heidelberg, under the direction of Jorg Schaefer. Consolidation works and clearing are carried out at intervals by the 23rd Ephorate at the "Villa of the Lilies" and the sanctuary of Zeus.

The most important monuments of the site are:

- "Villa of the Lilies". Minoan villa with paved corridors, "polythyra" (pier-and-door partitions), shrine, kitchen and rooms decorated with wall-paintings depicting blossomed lilies. - Sanctuary of Zeus Thenatas. It is situated on the hill of Palaiochora and has a peribolos surrounding a circular altar of ashes. A wall built of ashlar blocks, dated to the MM II period, is visible today next to the sanctuary of Zeus. - Building C-"Megaron". Minoan building divided into two separate rooms by a partition wall. It was used until the 14th century B.C.

- Complex E. Part of a Late Minoan settlement to the west of the hill of Palaiochora. A section has been submerged in the sea and the preserved complex is divided into two large wings; the east includes storerooms and the west is occupied by a shrine and a deposition pit. - Complex F (Mycenaean settlement). It is also part of a settlement, possibly the same as that of "Complex E". It consists of irregular architectural complexes, with rooms employed for the storage of amphoras, a small temple (?) and an open courtyard. - Houses of the Venetian period. The settlement called Mesovouni is located on the hill of Palaiochora and was destroyed in the first years of the Turkish occupation