Various archeological studies in the region prove that Ayvalık and its environs were inhabited as early as theprehistoric ages. Joseph Thacher Clarke believed that he had identified it as the site of Kisthene, mentioned byStrabo as a place in ruins at a harbour beyond Cape Pyrrha Kisthene was further identified by EnginBeksacofTrakya University, as KizCiftlik, near the centre of Gomeç.
The Ayvalık Region was studied by Beksac in his survey of the Prehistoric and Protohistoric settlements on the Southern Side of the Gulf Of Adramytteion. The survey showed different settlements near the centre of Ayvalık which appear generally to relate to the Early Classical Periods. However, some settlements near the centre of Altınova were related to the Prehistoric Period, especially the Bronze and Iron Ages. Kortukaya, identified by Beksac, in his survey project in the 1990s and early 2000s, aids understanding of the interaction between the peoples of the interior and of the coast. Kortukaya is one of the most important settlements, along with another settlement, Yeniyeldeginmeni, near the centre of Altınova.
Traces of a hillfort were identified by Beksac on Ciplak Ada or Chalkys. Some Late Bronze Age and Early Iron Age Pottery fragments related to the Aeolians were found on the same island. Two tiny settlements, near the centre of Ayvalık were settlements in the Peraia of Mytillini.
Pordoselene, near the centre of Ayvalık, was also an important settlement ın Antiquity. The remnants, were on the eastern part of the Island of Cunda or Alibey, near the sea. All the archaeological data was related to the Classical and Medieval Ages.
The constant threat posed by piracy in the region during the previous ages did not allow the islet settlements to grow larger and only Cunda Island (alternatively known as Alibey Island, known among the Greeks as Moschonisia, literally "The Perfumed Island") could maintain a higher level of habitation as it is the
