Momentum-resolved high-resolution electron energy loss spectroscopy has been used to probe the phonon dispersion of periodically rippled graphene grown on Ru(0001). Optical phonons in this system show anomalies with respect to other graphene/metal interfaces. Novel modes with weak intensity are observed at ∼86 and ∼150 meV. Moreover, the dispersion relation of the highest optical branches in the Γ-K direction strongly deviates from the expected behavior. These unusual features in the phonon dispersion should be related to the corrugated and chiral structure of the graphene overlayer on Ru(0001).