The eastern Alpine crust has been shaped by the continental collision of the European and Adriatic plates beginning at 35 Ma and was affected by a major reorganization after 20 Ma. To better understand how the eastern Alpine surface structures link with deep seated processes, we analyze the depth‐dependent seismic anisotropy based on Rayleigh wave propagation. Ambient noise recordings are evaluated to extract Rayleigh wave phase dispersion measurements. These are inverted in a two step approach for the azimuthally anisotropic shear velocity structure. Both steps are performed with a reversible jump Markov chain Monte Carlo (rj‐McMC) approach that estimates data errors and propagates the modeled uncertainties from the phase velocity maps into the depth inversion. A two layer structure of azimuthal anisotropy is imaged in the Alpine crust, with an orogen‐parallel upper crust and approximately orogen‐perpendicular layer in the lower crust and the uppermost mantle. In the upper layer, the anisotropy tends to follow major fault lines and may thus be an apparent, structurally driven anisotropy. The main foliation and fold axis orientations might contribute to the anisotropy. In the lower crust, the N‐S orientation of the fast axis is mostly confined to regions north of the Periadriatic Fault and may be related to European subduction. Outside the orogen, no clearly layered structure is identified. The anisotropy pattern in the northern Alpine foreland is found to be similar compared to SKS studies which is an indication of very homogeneous fast axis directions throughout the crust and the upper mantle.