We discuss the structure of the present Hellenic subduction zone. We show that the present Hellenic subduction zone was formed at about 15 Ma when it started to consume the Mediterranean lithosphere and to form the large accretionary wedge that covers a large part of the eastern Mediterranean. We establish that there is independent evidence that the very large Hellenic Trough that it created was formed simultaneously. Shortly before, an 8–10 km thick backstop that extends 200 km southward, where it presently abuts the African margin, was put into place. We reconstruct the northern margin of the eastern Mediterranean Sea prior to the Hellenic subduction in a new and independent way. The faults recently identified by Sachpazi et al. (2016a. Geophysical Research Letters, 43: 651–658) and Sachpazi et al. (2016b. Geophysical Research Letters, 43: 9619–9626) within the Hellenic seismic slab are a key element of our reconstruction. This is because the slab, which is part of the Nubia plate, is rigid and the faults within it coincide with the lines of slip congruent with the relative motion of the Aegean block over it. These faults demonstrate that about 400 to 500 kilometers of eastern Mediterranean lithosphere have been subducted with essentially the same southwestward direction of motion during the last 15 Myr. Our reconstruction shows that before the onset of the Hellenic subduction, the northern margin of the eastern Mediterranean Sea coincided with a major Jurassic transform fault that limited the eastern Mediterranean to the north during its formation in the Jurassic and Early Cretaceous as proposed in part 1. We discuss the implications of this reconstruction on the Neogene evolution of the Anatolia–Aegea block and its geodynamics.

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