1. A scanning microscope system comprising: an optical microscope observation unit that irradiates a sample with excitation light, and forms an optical image from fluorescence emitted from the sample; a scanning map creator that creates a scanning map indicating a scanning region in which a substance to be scanned exists in the sample, based on brightness of pixels of the optical image; and a flying spot scanning observation unit that scans the scanning region of the sample with laser beam, and forms a scanning image based on fluorescence emitted from the sample.