Current models for the Oligo-Miocene post-orogenic back-arc extension of the Aegean domain suggest that stretching is accommodated by two bivergent detachment systems of opposing shear sense. The co-existence in the Eocene of a top-to-the-S thrust at the base of the Cycladic Blueschists unit and top-to-the-N extensional shear zones at the roof raises the problem of differentiating synorogenic and post-orogenic deformations with similar directions and shear senses. Based on structural field data, this study shows that the post-orogenic deformation recorded in the Southern Cyclades is extremely asymmetric as the Cycladic Blueschists unit is pervasively affected by top-to-the-N shearing deformation distributed on four main shear zones. All activated in greenschist-facies conditions, some of these shear zones operated in the brittle regime during the final part of the exhumation. The Cycladic Blueschists/Cycladic Basement contact displays clear polyphased deformation with the preservation of top-to-the-S thrust kinematics. Thermal structure of the Cycladic Blueschists unit with regards to position of ductile shear zones was retrieved using the Raman Spectroscopy of Carbonaceous Material peak-metamorphic temperatures. This study shows a series of major metamorphic gaps accommodating an upward and stepwise decrease of more than 200 °C within the Cycladic Blueschists unit. Pressure-temperature estimates show that only lower parts of the Cycladic Blueschists unit recorded ca. 18–20 kbar for 530 °C peak-conditions. While flanking the West Cycladic Detachment System, which shows a top-to-the-S shear sense, the Southern Cyclades are dominated by a top-to-the-N non-coaxial shearing. Deformation is therefore genuinely asymmetric in the center of the Aegean domain.