Some of the oldest rocks in Greece are from the Paleozoic and are usually metamorphosed with no fossils. The Rhodope Massif spans the northern mainland, divided into amphibolite schist and gneiss, with comparatively recent granite intrusions from the Oligocene and Miocene. West of the Strymonas River is the Serbo-Macedonian Massif, covering the Chalkidiki Peninsula with thick marble and gneiss, with granite intrusions.
Alpine cycle sedimentary rocks are situated between the European hinterland in the Rhodope Massif and Serbo-Macedonian Massif and northern fore-region of the African plate. External zones include the Paxi Zone, encompassing the islands in the Ionian Sea with dolomitzed limestone from the Jurassic and Cretaceous-Miocene marl and gypsum. The Ionian Zone spans much of western Greece with Triassic evaporites overlain by Jurassic neritic limestones. During the Toarcian, extensive block faulting differentiated the Ionian Basin. Extensional faults were reactivated during the Eocene Alpine orogeny. The Ionian Zone is thrust westward over the Preapulian Zone and overlain by molasse facies.
The Gavrovo-Tripolis Zone underlies Crete, the Dodecanese islands and much of the western mainland. Bauxites indicate a dry time in the Eocene and Oligocene flysch unconformably overlies older carbonates. The Peloponnesus and Crete regions of the zone are overthrust on the Plattenkalk unit. Normal faults with four kilometers of displacement are not uncommon although folding is limited—tectonic activity picked up in the Oligocene. 
Internal zones span between the Serbo-Macedonian Massif and external zones:
The Axios Zone, also known as the Vardar Zone, represents the closing of the Axios Ocean and separates the Pelagonian zone from the Serbo-Macedonian Massif. Clastic sediments from the Paleozoic and Mesozoic ophiolites and sediments are common. Geologists subdivide it into the calc-schists, granite, diabase, chert and ophiolite of the Paeonias subzone and the acidic volcanic rocks and limestone of the Triassic-Jurassic Paikon subzone (an old island arc). The silicified ophiolites of the Almopias subzone, bordering the Pelagonian zone to the northeast represents an old ocean trench. 
Neogene sediment deposited after the Alpine cycle outcrops widely. The Mesohellene Trough, Epirus-Arkanania basin and Cycladic Basin are all examples of molasse basins from the early Miocene. The Ionian Islands basin is part of the Preapulian Zone and may only have had an interruption in sedimentation in the late Miocene into the Pliocene. Most sediments in other Neogene basins are marine, but the Aegean Islands basin is filled with continental sediments. As the molasse basins filled during Burdigalian and Langhian times, the uplift of the Pindus Cordillera caused nappe formations to slide onto metamorphic rocks of the Cyclades. In the Tortonian, arc fracturing brought subsidence of the Cretan Basin. Inland basins preserved numerous mammal fossils such as the Pikermi site north of Athens in continental clay.
Volcanic activity in the Aegean began in the Neogene and Quaternary. Volcanoes in western Thrace, Limnos and Samothrace are on the edge of the Rhodope Massif, while the Aegean volcanic arc borders the Menderes Massif and Attico-Cycladic Massif. The Neogene Santorini volcanoes erupted in the Holocene, destroying the Mycenaen civilization. Interior basins hold thick lakebed sediments from the Quaternary, indicating oscillation between cold desert conditions and wet interglacials. Travertine springs often preserve more recent fossil assemblages. Near Corinth, brackish Black Sea water invaded during the Middle Pleistocene, although for the most part, the islands and water area of the Aegean did not change the during the ice ages. 
Herodotus recognized a bitumen well at Limin Keri on the southern end of Zakynthos Island. Onshore oil exploration began in 1938 and moved offshore in 1970. The Prinos Anticline offshore was found to contain oil under Miocene rocks. 
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