The complex structure of the North-East Greenland margin is the consequence of two rifting events: the initial separation of Greenland and Scandinavia around 56 Ma, and the dispersal of the Jan Mayen microcontinent from Greenland around 33 Ma. The latter event might have been driven by the arrival of the Iceland Plume beneath the east coast of Greenland. The boundary between these two rifting events is the Jan Mayen Fracture Zone. While seismic lines north of this pronounced topographic structure document the crustal variations in detail, this is not the case south of it. The data show no indications that the lower crust hosts a large, high velocity body as has been found north of the fracture zone. A 500 km long seismic transect, which starts in Kong Oscar Fjord, provides a detailed view of the crustal structure just south of the Jan Mayen Fracture Zone. The transect includes parts of the Caledonian crust of Greenland, and crosses the present-day shelf and the oceanic crust formed since the separation of the Jan Mayen microcontinent. The seismic refraction line shows a constant ~9 km thick oceanic between the extended continental margin and the mid-ocean ridge. Indications for a 3 km thick high-velocity lower crustal body are observed within the continent-ocean transition zone. While such high velocity crust is ubiquitous beneath the shelf to the north of the fracture zone, to the south it only occurs beneath Mesozoic basins that have been attributed to extensional collapse of the Caledonian orogeny in East Greenland. Inline with earlier interpretations of high velocities in the lower crust of extended continental margins, we suggest that Kong Oscar Fjord is underlain by the products of excess magma production that were focused along the Jan Mayen Fracture Zone during the breakup of the Jan Mayen microcontinent from Greenland. In strong contrast north of the Jan Mayen Fracture Zone only thin oceanic crust is present. While the Greenland Basin has crustal thicknesses up to 4 km and formed during slow to ultraslow spreading rates, all geophysical data north of the Greenland Ridge indicate a formation of the Boreas Basin at ultraslow spreading rates. These observations indicate that a possible thermal mantle anomaly, which caused/fed the East Greenland continental flood had a limited size and was located close to the Kong Oscar/Kajser Franz Josef fjords. In summary, the existing crustal data support models in which the Jan Mayen Fracture Zone plays an important role for the regional magmatism off East Greenland.