A super-resolution fluorescence microscopy using two-color laser beams was proposed. The microscopy is based on the combination of two-color fluorescence dip spectroscopy and a phase modulation technique for the laser beam. By applying the proposed technique to a laser-scanning microscope, a fluorescence image of a sample can be observed with a spatial resolution overcoming the optical diffraction limit. To demonstrate validity of the microscopy, we constructed a scanning microscope system using commercial nano-second pulse lasers. An image of micro beads containing dye molecules was observed by the microscopy. We succeeded in obtaining the image with a resolution overcoming the diffraction limit in nano-meter scale region. The experimental data showed that the resolution was improved three times at least. The microscopy is expected to be an appropriate analysis method for the samples with nano-meter scale structures.