The geological setting of Samothraki Island is characterized by Jurassic ophiolites (mostly basaltic pillow lavas, and an igneous suite that ranges from gabbro to plagiogranite) of the Circum-Rhodope belt, and younger sedimentary rocks locally subjected to low-grade to greenschist-facies metamorphism. They are covered by volcanics (ranging from basalts to rhyolites) and intruded by granitoids of Oligocene to Miocene age.
The oldest sedimentary rocks are coarse breccias and conglomerates interbedded with polymictic sandstones and siltstones, and locally, thin limestones. All these rocks underwent strong deformations and low-grade to greenschist facies metamorphism. The petrography of the pebbles indicates a dual provenance. (A) Almost all ophiolitic petrographies are present: basalts and dolerites (pillow-lavas included), gabbros, diorites, plagiogranites. (B) Pebbles (dominant in the upper parts of the section) from low-grade metamorphics of the Circum-Rhodope flysch or of shallow marine origin (coral-bearing limestone included). Coral remains from a conglomerate pebble found at Aghios Georgios have been determined in the past as Late Jurassic to Early Cretaceous. The age of the conglomeratic formation itself is uncertain – it may be Late Cretaceous or Palaeogene.
The Palaeogene terrigenous formation of Samothraki is referred to the Upper Eocene. However, the lowermost parts of the profile may be of pre-Priabonian, and the uppermost ones, of Early Oligocene age. The formation covers unconformably and transgressively the ophiolites or follows over the conglomeratic formation. Sandstones and siltstones with shaly and limestone interbeds are dominant, in the middle parts of the section being interbedded with thick limestones (packstone and wackestone) rich in foraminifers, corals, corallines, bryozoans, echinoderms, gastropods and bivalves. Locally (Kastro at Hora), the section begins directly with the limestone beds hinting at possible reef facies wedging out inside the sandy molasses facies, and passing into olistostrome. The sedimentary microfacies of the limestones correspond to a proximal middle carbonate platform, and may be correlated with similar facies in Thrace. The limestone beds are usually strongly tectonized, and in the basal parts and along contacts with the basement have been subjected to low-grade metamorphism. Near the Kastro at Hora, thin Palaeogene limestone beds are observed as tectonic insertions within the ophiolites of the basement. Strongly fractured limestone interbeds are often boudinaged, and parts of the section pass into mélange of mixed sedimentary and tectonic origin.
Comparisons with the Palaeogene rock sequences and environments of nearby Rhodope and Thrace basins enable reconstructions of the palaeogeography and palaeogeodynamics. Cretaceous crustal thickening during the collisional orogeny was followed by extensional collapse of the orogen, and formation and closure of several Palaeogene troughs. The formation of the Thracian trough began in Palaeocene times, and continued throughout the Eocene. Locally in Thrace (east of Xanthi) and Samothraki, intense south-vergent thrusting is recorded. During Late Eocene time, lacustrine basins developed in the Rhodope area, and were followed by early Oligocene transgression accompanied by volcanic activity. The evolution of this Oligocene intracontinental volcanic island arc (probably formed by extensional collapse of a “plateau” overriding a detached subducting slab) ended with Late Oligocene regression, transtension along major fault belts, and Early Miocene transpression.