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The average anisotropy beneath Anatolia is very strong and is well constrained by shear-wave splitting measurements. However, the vertical layering of anisotropy and the contribution of each layer to the overall pattern is still an open question. Here we construct anisotropic phase-velocity maps of fundamental-mode Rayleigh waves for the Anatolia region using ambient noise seismology and records from several regional seismic stations. We find that the anisotropy patterns in the crust, lithosphere and asthenosphere beneath Anatolia have limited amplitudes and are generally consistent with regional tectonics and mantle processes dominated by the collision between Eurasia and Arabia and the Aegean/Anatolian subduction system. The anisotropy of these layers in the crust and upper mantle are, however, not consistent with the strong average anisotropy measured in this area. We therefore suggest that the main contribution to overall anisotropy likely originates from a deep and highly anisotropic region round the mantle transition zone.