Misalignment between the Hartmann–Shack wavefront sensor (HSWFS) and the
deformable mirror (DM) will degrade the performance of an adaptive optics (AO) system
severely. In this paper, a method of measuring the misalignment between the HSWFS and
the DM, which is called the marked actuators of the DM, is presented. The misalignments
are divided into different groups and analyzed theoretically. In addition, a 45-element
adaptive optics system is constructed to validate the accuracy of the method
experimentally. As a consequence, the experimental result agrees well with the theoretical
ones.