Seismic anisotropy data are often used to resolve rock textures and deformation in the crust based on compilations of rock properties that may not be representative of the local geology. In this paper, we use teleseismic receiver functions jointly with in situ rock property data to constrain the seismic structure and anisotropy of the crust in the Cyclades, Greece, located in the back‐arc region of the Hellenic subduction zone. The receiver function data indicate that the Moho is relatively flat at 25 km depth toward the south and deepens to 33 km in the north, consistent with previous studies, and reveal an intracrustal discontinuity at depths varying from 3 to 11 km, mostly observed in the south central Aegean. Harmonic decomposition of the receiver functions further indicates the presence of both shallow and deep crustal anisotropy related to crustal structures. We model synthetic receiver functions based on constraints from in situ rock properties that we measured using the electron backscatter diffraction technique. Our results indicate that the shallow upper crustal layer is characterized by metapelites with ~5% anisotropy, underlain by a 20 km thick and possibly anisotropic layer of high‐pressure rocks comprising blueschist and eclogite and/or restitic crust resulting from magmatism. This study demonstrates the importance of rock textural data in the interpretation of seismic velocity profiles.