Multilayered oxide heteroepitaxial systems, including that of a 1-nm-thick Y2O3-stabilised ZrO2 (YSZ) sandwiched between layers of SrTiO3 (STO) [1], have been a subject of much interest lately due to their significantly enhanced ionic conductivities as compared to the bulk materials. We aim to provide the foundation for understanding this increase in conductivity by considering the atomic configurations at the interfaces of such systems, specifically a ZrO2/STO multilayer system. Possible stable lattice structures of pure ZrO2 in the system are explored using a genetic algorithm in which the interatomic interactions are modelled by simple pair potentials. The energies of several of the more stable of these structures are then evaluated more accurately within density functional theory (DFT). We find that the fluorite ZrO2 phase is unstable as a coherently strained epitaxial layer in the multilayer system. Instead, anatase-, columbite-, rutile-, and pyrite-like ZrO2 epitaxies are found to be more stable, with the anatase-like epitaxy being the most stable structure over a wide range of chemical potential of the components. We also find a high energy metastable structure resembling the tetragonal fluorite structure which is predicted by DFT to be stabilised by SrO-terminated STO but not by TiO2-terminated STO.