Intramolecular proton transfer in malonaldehyde (MA) has been investigated by density functional theory (DFT). The DFT results were used for the construction of a high quality semiempirical potential energy surface with a reparametrized PM3 Hamiltonian. A two-step reparameterization procedure is proposed in which (i) the PM3-MAIS core–core functions for the O–H and H–H interactions were used and a new functional form for the O–O correction function was proposed and (ii) a set of specific reaction parameters (SRP) has been obtained via genetic algorithm optimization. The quality of the reparametrized semiempirical potential energy surfaces was tested by calculating the tunneling splitting of vibrational levels and the anharmonic vibrational frequencies of the system. The applicability to multi-dimensional dynamics in large molecular systems is discussed.