The antiphase domain structure in epitaxial Fe 3 O 4 films determines its physical properties such as superparamagnetism, resistivity, and magnetoresistance. A good knowledge and control of the domain sizes in these films is therefore of utmost importance. We report on the finding that the antiphase domain boundaries anneal out via a diffusive mechanism at relatively low temperatures. This has been demonstrated by postannealing the films at 250°C, 300°C and 350°C. The boundary migration process is a thermally activated process with an activation energy of 26 kJ/mol ͑250 meV͒. We have further studied the domain size in epitaxial Fe 3 O 4 films as a function of growth parameters. A linear relationship has been obtained for the logarithm of the domain size versus the inverse of the growth temperature ͑in the range of 125°C to 300°C), which supports the diffusional mechanism. The domain size is not influenced by the iron flux, but does depend on the oxygen flux. This suggests that the critical nuclei are pairs of iron and oxygen atoms and that iron is more mobile than oxygen.