An important geological structure appears in the area of Kryfti, which is typical for the way the rocks are formed and gives evidence for the contribution of rift tectonics to the North Aegean.

In the area there are impressive images of tectonic mixtures (mélange), geological schematics that display a chaotic structure, as smaller or larger pieces of rock meet mixed in with a fundamental mass. They consist mainly of crystalline limestones, quartz-mica schists, green schists  and less of ophiolites.

Ophiolites are rocks that formed from rising magma at the bottom of the Tethys ocean as it opened up and was being created. About 150 million years ago the geological conditions changed. The large landmasses of Laurasia and Gondwana began to converge. The rocks that formed the Tethys ocean floor were compressed, uplifted, and pushed up onto the Eurasian continental margin, hundreds of kilometers away from their original location, overriding other rocks that today lie below the ophiolitic rocks of the Tethys ocean floor.

The tectonic mixtures were created during emplacement of the ophiolitic mass on the continental margin. The limestone blocks of the background (like the massif of Panagia Kryftis), were detached from the continental margin during the emplacement of the ophiolites and mixed with them. Today they dominate the area as they appear trapped within the tectonic mixtures.

The rocks of the area have been strongly affected by a large horizontal displacement fault with a NE-SW direction, displaying the impressive vertical gradients of the tectonic mixtures in a zone hundreds of meters wide. This fault is responsible for the creation of the canyon and the hot springs that erupt in the area. The geological structure (type of rocks, fault etc.) is also responsible for the creation of caves that characterize the area, one of which has been used for the chapel of Panagia Kryfti.

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