The results of experimental and theoretical studies of phonon modes in short-period (GaN)m(AlN)n superlattices (SLs) grown by MOVPE and PA MBE on the (0001) Al2O3 substrate are reported. Using a comprehensive group-theoretical analysis, the genesis of the SL vibrational modes from the modes of bulk AlN and GaN crystals has been established, which is important for interpreting the SL Raman spectrum. In the framework of Density Functional Theory, the lattice dynamics and the structural properties of (GaN)m(AlN)n SLs (m+n⩽12) were studied. An analysis of the eigenvectors of the phonon modes made it possible to reveal their microscopic nature. We established that the E(TO) modes are localized in the layers constituting the SL. It is shown that the localized nature of this mode is kept even in the SLs with the thinnest layers (m+n=4). In turn, the A1(TO) mode demonstrates a delocalized nature and reflects the averaged characteristics of the SL as a whole. A combined analysis of the ab initio calculations and Raman data was performed. Thus, the above studies open new possibilities for analyzing the structural properties of GaN/AlN SLs by Raman and IR spectroscopy.