A microscope system (100) includes a microscope (10) and an observation unit (20) provided separately from the microscope. The microscope includes a microscope objective lens (3), an image pickup element (31) disposed at a position at which an image is formed through the microscope objective lens, and a first control apparatus (32) connected with the image pickup element. The observation unit includes a second control apparatus (21), a display device (22, 22a, 22b) connected with the second control apparatus, and a magnifier optical system (25a, 25b) arranged at a predetermined distance from the display device. The microscope system further includes a communication apparatus (21) for communication between the first control apparatus and the second control apparatus so that an image picked up by the image pickup apparatus is displayed on the display device.