Abstract Atomic structures of three Ga 2Se 3 epilayers grown on GaAs(100) or ZnSe(100) epilayers by molecular beam epitaxy were studied by transmission electron microscopy. A new vacancy ordered structure was found in the heteroepitaxial interface regions of Ga 2Se 3 epilayers. The ordered structure is described as an alternate stacking of two types of Ga planes in the growth direction. One half of the sites are vacancies in one type of Ga plane, while the other type of Ga plane is fully occupied by Ga atoms. Comparison of three Ga 2Se 3 epilayers indicates a strong influence of surface chemistry of substrate epilayers on the formation of the vacancy ordering. A highly developed two-dimensional ordering has occured in the epilayer grown on a GaAs(100) surface with (4 × 3) rereconstructions.