Provided is a microscope system that including: a plurality of image-capturing sections that are provided in a microscope to capture a plurality of lights from a specimen; a capture-condition setting section that allows a user to set an image-capturing order of the plurality of groups into which the lights are classified, and the image-capturing sections for image-capturing of the lights; and a control section that causes the microscope to perform image capturing of the lights according to contents set in the capture-condition setting section. The capture-condition setting section has a table in which an first axis indicates the groups and a second axis indicates the image-capturing sections, and a plurality of cells that are each associated with one of the groups and one of the image-capturing sections are arrayed in a matrix; and captured items that indicate image-capturing of the lights are set in the cells.