A microscope system (100, 300) as an optical microscope system for observing a specimen, the microscope system comprising: an imaging optical system that forms an image of transmitted light or reflected light from the specimen; an illumination light source that illuminates illumination light to the specimen; an illumination optical system that has a first spatial light modulation element (90, 93, 94, 390), which changes the intensity distribution of the illumination light at a conjugate position of a pupil of the imaging optical system, and illuminates light, which is originated from the illumination light source, on the specimen; an image sensor that detects light through the imaging optical system; and characterized in that the microscope system further comprises a calculation section that performs an estimating process that estimates structure or characteristic information of the specimen and performs afterwards a calculation of an intensity distribution of the illumination light appropriate for observation of the specimen on the basis of the intensity distribution of the illumination light formed by the first spatial light modulation element and output data detected by the image sensor, wherein the estimating process includes estimates of: (i) phase information of the specimen, microscopic structure information, or information with respect to a wavelength of illumination light on the basis of output data detected by the image sensor with two rays of illumination light formed by the first spatial light modulation element and of which coherence factors are different from each other, the coherence factor being a ratio of a numerical aperture NA' of the illumination light formed by the first spatial light modulation element to a numerical aperture NA of the imaging optical system; or (ii) phase information of the specimen or spatial frequency information on the basis of the output data with two rays of illumination light formed by the first spatial light modulation element and, each of which is a monochromatic point light source where the coherence factor thereof is equal to 0, one of the two point light sources being disposed at an optical axis and another one being disposed separate from the optical axis. an imaging optical system that forms an image of transmitted light or reflected light from the specimen; an illumination light source that illuminates illumination light to the specimen; an illumination optical system that has a first spatial light modulation element (90, 93, 94, 390), which changes the intensity distribution of the illumination light at a conjugate position of a pupil of the imaging optical system, and illuminates light, which is originated from the illumination light source, on the specimen; an image sensor that detects light through the imaging optical system; and characterized in that the microscope system further comprises a calculation section that performs an estimating process that estimates structure or characteristic information of the specimen and performs afterwards a calculation of an intensity distribution of the illumination light appropriate for observation of the specimen on the basis of the intensity distribution of the illumination light formed by the first spatial light modulation element and output data detected by the image sensor, wherein the estimating process includes estimates of: (i) phase information of the specimen, microscopic structure information, or information with respect to a wavelength of illumination light on the basis of output data detected by the image sensor with two rays of illumination light formed by the first spatial light modulation element and of which coherence factors are different from each other, the coherence factor being a ratio of a numerical aperture NA' of the illumination light formed by the first spatial light modulation element to a numerical aperture NA of the imaging optical system; or (ii) phase information of the specimen or spatial frequency information on the basis of the output data with two rays of illumination light formed by the first spatial light modulation element and, each of which is a monochromatic point light source where the coherence factor thereof is equal to 0, one of the two point light sources being disposed at an optical axis and another one being disposed separate from the optical axis. (i) phase information of the specimen, microscopic structure information, or information with respect to a wavelength of illumination light on the basis of output data detected by the image sensor with two rays of illumination light formed by the first spatial light modulation element and of which coherence factors are different from each other, the coherence factor being a ratio of a numerical aperture NA' of the illumination light formed by the first spatial light modulation element to a numerical aperture NA of the imaging optical system; or (ii) phase information of the specimen or spatial frequency information on the basis of the output data with two rays of illumination light formed by the first spatial light modulation element and, each of which is a monochromatic point light source where the coherence factor thereof is equal to 0, one of the two point light sources being disposed at an optical axis and another one being disposed separate from the optical axis.