A substrate bonding apparatus is equipped with a first table that holds one wafer of two wafers, a stage device that holds the other wafer in an orientation capable of opposing to the one wafer and that is movable at least within an XY plane, an interferometer system that measures positional information of the stage device within the XY plane, a first mark detection system that can detect subject marks including alignment marks on the other wafer held by the stage device, and a second mark detection system fixed to a part (the second table) of the stage device that can detect subject marks including alignment marks on the one wafer held by the first table.