For a thorough exploration of the subsurface beneath Northern Morocco the implementation of several temporary seismic stations gave rise to a first opportunity to study from close the Rif and Atlas domains structures. These transects are characterized by the complexity of their seismotectonic model, despite their moderate seismic activity that is associated to the convergence between the two lithospheric plates, respectively Eurasia and Africa. We take advantage of four years of continuous data (2011–2014) emanating from a dense coverage including more than 250 stations from permanent and temporary ronal networks, to produce tomographic maps of a fine resolution in order to identify structures and spot heterogeneities within the crust. The outcomes of group and phase velocities are obtained from empirical Green functions produced by performing the cross correlation of long ambient noise sequences available between pairs of stations dispatched across Northern Morocco and the surrounding areas. In order to obtain more accurate information, the cross-correlations are stacked in all-time series and are used to get the group and phase velocity dispersion curves from Rayleigh waves. The measurements of uncertainties based on seasonal variations are estimated from the subsets temporal data. As a result, we suggest for the first time in the area, a prominent imaging of the ambient seismic noise tomography of 4–40 s period using Rayleigh waves. A set of these maps is exhibited and interpreted with the aim of describing the characteristics of the crust and discern the correlations between and throughout different major geological features like sedimentary basins, Meseta plateau, Atlas Ranges.