The atomic structure of antiphase nanodomains in Fe-doped SrTiO3 films is revealed directly by aberration-corrected scanning transmission electron microscopy. In particular, the crystallographic translation vector between the antiphase nanodomains and the matrix is determined to be a/2 [0 1 1], distinct from a/2 [0 1 1] for the well-known Ruddlesden-Popper (RP) planar faults in perovskite structure. The antiphase boundaries lie mostly in the {1 0 0} planes and partially in the {1 1 0} planes. The atomic structure of the antiphase boundaries is found to consist of chains of edge-sharing TiO6 octahedra implying a local Ti-enrichment, which is in strong contrast to local Sr-enrichment at the RP type antiphase boundaries.