1. A microscope system used for acquiring an image of a sample comprising: a light guiding optical system having an objective lens to which an optical image of the sample is made incident; a focus controller; a first image pickup device configured to acquire an image of the sample, wherein the first image pickup device is arranged along an image acquisition optical path optically coupling the first image pickup device and the sample; a beam splitter configured to split an optical image of the sample to the image acquisition optical path and a focus control optical path; a splitting optical system configured to split an optical image of the sample propagating along the focus control optical path to a plurality of optical paths having different optical lengths; and a second image pickup device having a plurality of image pickup areas, wherein the second image pickup device is disposed so as to receive, at each of the image pickup areas, respectively, the optical image of the sample propagating along each of the optical paths having different optical lengths; wherein the focus controller analyzes the images received by the second image pickup device and acquires focus control information, the focus controller adjusts a focal point on the basis of the focus control information, and the image acquisition of the sample by the first image pickup device and focus control of the first image pickup device are simultaneously carried out.