A microscope apparatus comprising: a light source configured to generate a laser beam; a collimator lens configured to convert the laser beam generated by the light source into a substantially plane wave; a spatial light modulator configured to modulate a wavefront of the laser beam converted into a substantially plane wave, wherein the laser beam is made incident on the spatial light modulator by the collimator lens so as to illuminate an illuminated region that includes and is larger than a modulation region in which the laser beam is actually modulated by the spatial light modulator; a scanner that has two mirrors (6a, 6b) configured to independently pivot about two non-parallel axes, the scanner being configured to two-dimensionally scan the laser beam whose wavefront has been modulated by the spatial light modulator;and a relay optical system that is configured to guide the laser beam, whose traveling direction has been changed by the scanner, to an objective optical system and that is further configured to relay an image in the modulation region to an entrance pupil position of the objective optical system; and a control unit configured to pivot the mirrors (6a, 6b), characterized in that the control unit is configured to output a shape instruction signal to the spatial light modulator so that a surface of the modulation region of the spatial light modulator forms a preset shape, the surface shape of the modulation region of the spatial light modulator being such that it can modulate the wavefront of the plane wave incident on the modulation region and can focus it on one point at a focal position of the objective optical system, wherein the control unit further is configured to operate as a modulation-region adjusting unit which is configured to move the modulation region of the spatial light modulator within the illuminated region of the spatial light modulator while the mirrors (6a, 6b) are stationary, wherein the modulation-region adjusting unit is configured to move the modulation region such that an image of the modulation region at the pupil position of the objective optical system is moved in the direction opposite to the direction of movement of the image formed at the pupil position of the objective optical system when the mirrors (6a, 6b) are pivoted. a light source configured to generate a laser beam; a collimator lens configured to convert the laser beam generated by the light source into a substantially plane wave; a spatial light modulator configured to modulate a wavefront of the laser beam converted into a substantially plane wave, wherein the laser beam is made incident on the spatial light modulator by the collimator lens so as to illuminate an illuminated region that includes and is larger than a modulation region in which the laser beam is actually modulated by the spatial light modulator; a scanner that has two mirrors (6a, 6b) configured to independently pivot about two non-parallel axes, the scanner being configured to two-dimensionally scan the laser beam whose wavefront has been modulated by the spatial light modulator;and a relay optical system that is configured to guide the laser beam, whose traveling direction has been changed by the scanner, to an objective optical system and that is further configured to relay an image in the modulation region to an entrance pupil position of the objective optical system; and a control unit configured to pivot the mirrors (6a, 6b), characterized in that the control unit is configured to output a shape instruction signal to the spatial light modulator so that a surface of the modulation region of the spatial light modulator forms a preset shape, the surface shape of the modulation region of the spatial light modulator being such that it can modulate the wavefront of the plane wave incident on the modulation region and can focus it on one point at a focal position of the objective optical system, wherein the control unit further is configured to operate as a modulation-region adjusting unit which is configured to move the modulation region of the spatial light modulator within the illuminated region of the spatial light modulator while the mirrors (6a, 6b) are stationary, wherein the modulation-region adjusting unit is configured to move the modulation region such that an image of the modulation region at the pupil position of the objective optical system is moved in the direction opposite to the direction of movement of the image formed at the pupil position of the objective optical system when the mirrors (6a, 6b) are pivoted.