The lattice preferred orientation (LPO) of both muscovite and biotite were measured by electron backscatter diffraction (EBSD) and these data, together with the LPOs of the other main constituent minerals, were used to produce models of the seismic velocity anisotropy of the Alpine Fault Zone. Numerical experiments examine the effects of varying modal percentages of mica within the fault rocks. These models suggest that when the mica modal proportions approach 20% in quartzofeldspathic mylonites the intrinsic seismic anisotropy of the studied fault zone is dominated by mica, with the direction of the fastest P and S wave velocities strongly dependent on the mica LPOs. The LPOs show that micas produce three distinct patterns within mylonitic fault zones: C-fabric, S-fabric and a composite S–C fabric. The asymmetry of the LPOs can be used as kinematic indicators for the deformation within mylonites. Kinematic data from the micas matches the kinematic interpretation of quartz LPOs and field data. The modelling of velocities and velocity anisotropies from sample LPOs is consistent with geophysical data from the crust under the Southern Alps. The Alpine Fault mylonites and parallel Alpine schists have intrinsic P-wave velocity anisotropies of 12% and S-wave anisotropies of 10%.