This three-dimensonal seafloor magnetization data was derived from the magnetic anomaly data. To carry out the inversion for seafloor magnetization the MGL1309 magnetic anomaly grid was extended within a rectangular area using regional gridded values from Macnab et al. (1995) and ship data from Searle et al. (1998) regridded in ~1 km cells. The multibeam bathymetry grid was extended within the same rectangular area using satellite-predicted bathymetry (Sandwell et al., 2014) to fill areas outside the multibeam coverage and regridded in ~1 km cells. The grids were mirrored to minimize edge effects and a three-dimensional Fourier inversion for seafloor magnetization (Parker, 1972) was carried out using Mirone Software (Luis, 2007) assuming a 500 m source layer with magnetization direction given by the axial geocentric dipole. Five terms in the Fourier series were used in the inversion. The resulting values were masked to the extent of the MGL1309 multibeam grid. As the polarity transitions agreed well with two-dimensional reversal modeling of profile values no annihilator was added. The data file is in PDF format. It is cited in Martinez and Hey, 2017, and was generated as part of the project called Test Between Thermal and Tectonic Hypotheses for North Atlantic Seafloor Spreading Geometry Reorganization. Funding was provided by NSF award OCE11-54071.