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New geological and structural mapping combined with kinematic and amphibole chemistry analyses is used to investigate the deformation history of the Cycladic Blueschist Unit (CBU) on Sifnos Island (Cyclades, Aegean Sea). We concentrate on north Sifnos, an area characterized by exceptionally well-preserved eclogites and blueschists. Our data show that the early, main phase (D2) of ductile deformation in the CBU occurred synchronous with the transition from prograde to close-to-peak retrograde conditions. This deformation phase took place at middle Eocene and is related to ESE-directed thrusting that emplaced the metavolcano-sedimentary subunit over the Marble subunit. The subsequent exhumation-related (D3) deformation is characterized by gently NE-plunging folds and NE-directed contractional shear zones that formed parallel to the axial planes of folds. NE-directed shearing occurred under blue- schist and transitional blueschist-/greenschist-facies conditions during late Eocene–Oligocene and caused the restacking of the early nappe pile. We suggest that a mechanism of ductile extrusion of the CBU in a tectonic setting of net compression could explain better the recorded exhumation-related deformation than a mechanism of syn- and post-orogenic extension. Our new kinematic results in combination with previous works in the Cyclades area reveal a regional scale change in tectonic transport direction from (W)NW–(E)SE at Late Cretaceous–middle Eocene to (E)NE–(W)SW at late Eocene–Oligocene times. The observed change in transport direction may be governed by the relative motion of Africa with respect to Europe during Alpine orogeny.