In this study, we measured shear wave splitting (fast direction and delay time) from 5193 crustal earthquakes that occurred in the south Aegean that were recorded by 65 stations of the EGELADOS, GEOFON, and MedNet networks between November 2005–January 2007. We utilized the Multiple Filter Automatic splitting Technique (MFAST) that allows quick processing of thousands of events and obtained a total of 3732 high-quality measurements. In general, the majority of fast directions follows a trend of NNE-SSW or NNW-SSE, while the average delay time was found equal to 0.149 s. Analysis of the percentage of anisotropy with hypocentral depth indicates that the interval between 5−20 km exhibits up to 6% of crustal anisotropy with the majority of values being smaller than 4%. Comparison of the observed fast shear wave directions with the maximum horizontal stress (Shmax) shows that stress-induced anisotropy can explain the fast directions along the forearc (Peloponnese, Kythira strait, eastern Crete, Kasos, Karpathos, Rhodes) and SW Turkey. In the Cyclades most fast directions are significantly different from Shmax. Structural anisotropy is dominant in southern Peloponnese, in some parts of Crete and Karpathos. In Cyclades fast directions at several stations agree well with the stretching lineations along the exhumed metamorphic core complex and some major fault zones. A comparison of fast shear wave directions of crustal anisotropy with those of SKS mantle anisotropy shows good agreement in the forearc (Peloponnese, eastern Crete, Karpathos, Rhodes) as well as SW Turkey and suggests that the crust is deforming in the same direction with the mantle flow. This pattern becomes less clear in the Cyclades where stations near the metamorphic core complex exhibit good agreement, while others exhibit large deviations between the two fast directions and point to a possible decoupling of the two lithospheric units.