Ayvalik and Cunda are two small neighboring settlements on the Aegean Sea coast in northwest Anatolia. Ayvalik is a city on the shore parallel to the sea while Cunda is a small island that occurs north of Ayvalik. Until the Republican period Cunda was a settlement separate from Ayvalik but today is within the boundaries of the city of Ayvalik. In the Ottoman period up to the end of the 18th century Ayvalik was known as Kydonia and Cunda Island as Yuni-Yunda-Cunda-Moshanisia. Ayvalık became a city in 1773 and Cunda in 1862 but independent of each other; economic development speeded up and enriched these cities that were completely Rum (Turks of Greek origin) in population under Ottoman patronage. The wealth was reflected in the socio-cultural and architectural structure. Ayvalik especially became an active city to which academicians, men of religion, missionaries and artists came and with its cultural. Because the peoples of the Ottoman Empire wanted to be independent in the 19th century, political movements began in Ayvalik too. As a result of these the autonomy that had been given to the city was lifted, and a large portion of the Rums who lived there was sent to Midilli. These migratory movements of the Rums who returned to the city again with the pardon promulgated in 1832 were repeated a number of times until the Lausanne Agreement signed in the aftermath of World War I. With the Lausanne Treaty the forcible exchange of population between the Rums of Turkey and the Turks of Greece occurred between 1922 and 1935. The Rums who lived in Ayvalik and Cunda were settled in Greece and the Turks on the islands of Crete and Midilli that remained within the borders of Greece were settled in Ayvalik and Cunda. In the aftermath of the compulsory exchange and the groups that lived in these cities the social order completely changed but the architectural fabric and the economic structure part have been preserved until today in spite of changes. In the urban fabric of Ayvalik and Cunda settlements an understanding of streets that are generally grill-planned is predominant. Commercial and industrial buildings were on the shore areas and on the slopes and hills were houses and religious structures. Magnificent churches occur among the two- or three-story houses in the neo-classic style. In Ayvalık and Cunda and the surrounding area, nearly 20 churches and monasteries show the importance of these settlements as religious centers in the 19th century. However, some of these churches have been completely destroyed in coming to the present. Among those that have survived, leaving out the ones in ruins, those that have been repaired and are being used again are in the majority. The churches generally are being used as mosques because the structure of society and beliefs have changed (Kato Panagia, Agia Yanni and Agia Iorgi churches). Aside from this role, the Cunda Taksiyarhis Church, the importance of which is very great among the Rums (Turks of Greek origin), operates as a museum and the Agios Yannis Church serves as a library and museum. There are churches that still don’t function although repaired or haven’t been repaired. The purpose of this communiqué will be to research and document the problems in protecting and using the churches that remain as the symbol of a different religion in the aftermath of the change in the political, administrative and social order experienced in a historical settlement.