Graphene placed on hexagonal-boron nitride (h-BN) experiences a superlattice (Moiré) potential, which leads to a strong reconstruction of graphene’s electronic spectrum with new Dirac points emerging at sub-eV energies. Here we study the effect of such superlattices on graphene’s Raman spectrum. In particular, the 2D Raman peak is found to be exquisitely sensitive to the misalignment between graphene and h-BN lattices, probably due to the presence of a strain distribution with the same periodicity of the Moiré potential. This feature can be used to identify graphene superlattices with a misalignment angle smaller than 2°.