A theoretical study is presented of he equilibrium domain microstructure expected for a thin film grown epitaxially onto single-crystal substrate as a function of temperature, film thickness, and lattice misfit for the case when the film can undergo a structural phase transition. The theory treats the epitaxial interface at the level of the Frenkel-Kontorova model and takes into account domain-wall energies and bulk-elasticity effects in both the film and the substrate. Existing predictions for this problem by Roitburd are reproduced when the epitaxial interface is commensurate. Results are obtained for the general case when the interface is incommensurate. The corresponding domain structure generically involves multiple phases.