1. A microscope system comprising: a light guiding optical system containing optical splitting means for splitting an optical image of a sample into a first optical path for image acquisition and a second optical path for focus control; first image pickup means which is disposed on the first optical path and used to acquire a one-dimensional or two-dimensional first image based on an optical image split to the first optical path; second image pickup means which is disposed on the second optical path so that an optical path length in the light guiding optical system varies along a predetermined variation direction on the image pickup face thereof and is used to acquire a two-dimensional second image for focus control based on an optical image split to the second optical path; focus control means for analyzing the second image acquired by the second image pickup means and controlling the focal point for image pickup by the first image pickup means on the basis of the analysis result; and image acquisition control means for controlling acquisition of the first image acquired by the first image pickup means.