This paper deals with the analysis of the vibrational and crystallographic properties of CuInC2 sC=S,Sed chalcogenides. Experimentally, evidence on the coexistence in epitaxial layers of domains with different crystalline order—corresponding to the equilibrium chalcopyrite sCHd and to CuAu sCAd—has been obtained by cross section transmission electron microsopy sTEMd and high resolution TEM sHREMd. Electron diffraction and HREM images give the crystalline relationship f110gCHif100gCA and s112dCHis011dCA, observing the existence of a s112dCHis001dCA interphase between different ordered domains. The vibrational properties of these polytypes have been investigated by Raman scattering. Raman scattering, in conjunction with XRD, has allowed identifying the presence of additional bands in the Raman spectra with vibrational modes of the CA ordered phase. In order to interpret these spectra, a valence field force model has been developed to calculate the zone-center vibrational modes of the CA structure for both CuInS2 and CuInSe2 compounds. The results of this calculation have led to the identification, in both cases, of the main additional band in the spectra with the total symmetric mode from the CuAu lattice. This identification is also supported by first-principles frozenphonon calculations. Finally, the defect structure at the interphase boundaries between different polymorphic domains has also been investigated.