The Manihiki Plateau of the western Pacific is one of the world - wide greatest Large Igneous Province (LIP) on oceanic crust. It is assumed that the Manihiki Plateau was emplaced as the centerpiece of the “Super-LIP” Ontong Java Nui by multiple volcanic phases during the Cretaceous Magnetic Quiet Period. The subsequent break-up of Ontong Java Nui led to fragmentation of the Manihiki Plateau into three sub-plateaus, which all exhibit individual relicts of the “Super-LIP” break-up. We examine two deep crustal seismic refraction/wide-angle reflection profiles crossing the two largest sub-plateaus of the Manihiki Plateau, the Western Plateaus and the High Plateau. Modeling of P- and S-wave velocities reveals surprising differences in the crustal structure between the two sub-plateaus. Whereas the High Plateau shows a constant crustal thickness of 20 km, relicts of multiple volcanic phases and break-up features at its margins, the model of the Western Plateaus reveals a crustal thickness decreasing from 17 km to only 9 km. There is only little evidence of secondary phases of volcanic activity. The main upper crustal structure on the Western Plateaus consists of fault systems and sedimentary basins. We infer that the High Plateau experienced phases of strong secondary volcanism, and that tectonic deformation was limited to its edges. The Western Plateaus, on the contrary, were deformed by crustal stretching and underwent only little to no secondary volcanism. This indicates that the two main sub-plateaus of the Manihiki Plateau experienced a different geological history and have played their individual parts in the break-up history of Ontong Java Nui.