Detailed mapping and structural observations on the Cycladic Blueschist Unit (CBU) of Iraklia island integrated by detrital zircon (DZ) U-Pb ages elucidate the Mesozoic pre-subduction evolution and the Cenozoic orogenic events. Field data reveal that the Iraklia tectonostratigraphy includes a heterogeneous Lower Schist Unit juxtaposed against a Variegated Marble Unit and an overlying Upper Schist Unit. The contact is an extensional ductile-to-brittle-ductile, top-to-N shear zone, associated with the Oligo-Miocene exhumation. The DZ spectrum of the Lower Schist Unit characterized by Gondwanan/peri-Gondwanan provenance signatures points to Late Triassic maximum depositional ages (MDAs). A quartz-rich schist layer yielded Precambrian DZ ages exclusively, considered part of the pre-Variscan metasedimentary Cycladic Basement, equivalent to those observed on Ios island. A significant change occurred during the deposition of the Upper Schist Unit, revealing Late Cretaceous MDAs and a high amount of Late Paleozoic DZ ages, attesting to more internal Pelagonian source areas. The imprint of Paleotethyan vs. Neotethyan geodynamic events is revealed in the DZ U-Pb ages record. The Triassic DZ input demonstrates eroded volcanic material related to the final Paleotethys closure and the Pindos/CBU rift basin opening. Late Cretaceous metamorphic/magmatic zircons and ~48-56 Ma zircon rims constrain the onset of subduction and high-pressure metamorphism.