Based on the positions of a first marker and a second marker of a first substrate placed on a placing surface of a substrate placing table (1), a substrate processing apparatus makes the direction of a line connecting the first marker and the second marker accord with the moving direction of a gantry (2). The positions of the first marker and a third marker, in the state that the direction of the line connecting the first marker and the second marker accord with the moving direction, are stored in a storage section. After a second substrate is placed on the placing surface of the substrate placing table (1), the direction of a line connecting the first marker and the third marker on the second substrate is made to accord with the direction of a line connecting the first marker and the third marker calculated from the position of the third marker and the fourth marker on the first substrate stored in the storage section.