A microscope apparatus comprising a confocal microscope comprising a laser light source for emitting a laser beam, a scanner for moving the laser beam emitted from the laser light source to scan in a two dimensional manner, an object lens for focusing the laser beam moved by the scanner on a specimen and collecting fluorescent light generated in the specimen, a dichroic mirror for branching the fluorescent light that has been collected by the object lens and is returning back through the scanner, out from the optical path of the laser beam, a condenser lens for condensing the fluorescent light branched out by the dichroic mirror, a confocal pinhole positioned at the focal point of the condenser lens, and a photodetector for detecting the fluorescent light passing through the confocal pinhole; a planar illumination light source attached to the confocal microscope; a CCD; an image retrieval unit configured to control the confocal microscope and the CCD, receive a picture signal from the CCD, generate two-dimensional CCD image information from the retrieved picture signal, receive fluorescence brightness information from the photodetector, and sequentially store the received fluorescence brightness information in association with a position and an oscillation angle of the scanner so as to thereby generate two-dimensional confocal microscope image information; a time counting unit for counting an observation time; a storage unit for storing image information and other information acquired by the confocal microscope and the CCD, wherein the storage unit is configured for storing image information, when acquired by any one of the CCD and the photodetector, and timing information counted by said time counting unit, by having them associated with each other; an image display unit for displaying said image information; and an image specifying unit for specifying a certain type of image information displayed on the image display unit, wherein the image retrieval unit is configured for retrieving, based on the timing information stored in association with the certain type of image information specified by the image specifying unit, a different type of image information acquired by a different one of the CCD and the photodetector other than the one of the CCD and the photodetector that has acquired the specified type of image information, said different type of image information is associated with timing information that is close to the timing information stored in association with the certain type of image information specified by the image specifying unit, said image display unit displays the different type of image information retrieved by said image retrieval unit, the image retrieval unit is configured, when reception of the picture signal from the CCD is started, to associate the timing information received from the time counting unit at the same time of the reception with the generated CCD image information, and the image retrieval unit is configured, when the reception of the fluorescence brightness information from the photodetector is started, to associate the timing information received from the time counting unit at the same time of the reception with the generated confocal microscope image information.