The island of Milos is part of the South Aegean volcanic arc. The volcanic processes on Milos, which started ca. 3.5 Ma, have been studied in detail, but the limited outcrops of basement rocks have not yet been adequately investigated. We present new structural, petrological, and geochronological data that suggest that the basement rocks on Milos (Kiriaki complex) belong to the Cycladic Blueschist Unit, which underwent blueschist metamorphism at ∼8.5 kbar and 400 °C. The complex experienced pervasive ductile deformation in the Paleocene–Eocene, with top-to-the-S to -SW shearing. Recalculation of published data from eclogite pebbles that occur as detrital products in “Green Lahars” structurally above the Kiriaki complex yields contrasting metamorphic conditions of ∼19.5 kbar at 550 °C, suggesting that two nappes, the exposed Lower Cycladic Nappe and eroded relicts of the Upper Cycladic Nappe, exist on Milos. These nappes, which also occur on other Cycladic islands, are separated by the newly defined synorogenic Trans Cycladic thrust. Since Milos is located above the West Cycladic detachment system, the rocks escaped the postorogenic middle–late Miocene low-angled extensional overprint. While rocks in the footwall of the West Cycladic detachment system were experiencing ductile shearing, sediments were being nonconformably deposited on metamorphic rocks of the Kiriaki complex on Milos in the late Miocene. Most importantly, the postorogenic West Cycladic detachment system did not reactivate but instead crosscut synorogenic structures such as the Trans Cycladic thrust, which bends 90° at Milos, exhibiting a change from W-E– to N-S–trending stretching lineations.