A microscope apparatus includes an objective lens; a light source for outputting light with which a biological sample is irradiated via the objective lens; a shape acquisition unit for acquiring information on at least one of a surface shape of the biological sample and a structure directly under the surface of the biological sample; a hologram generation unit for generating aberration correction hologram data for correcting an aberration caused by the at least one on the basis of the information acquired by the shape acquisition unit; a spatial light modulator to which a hologram based on the aberration correction hologram data is presented and for modulating the light output from the light source; a photodetector for detecting an intensity of light generated in the biological sample and outputs a detection signal.