We report on a novel technique of multi-spectral two-photon-excited fluorescence microscopy by use of broadband supercontinuum light. A supercontinuum in the near-infrared region is generated in a 4.5-min-long photonic crystal fiber using a Ti:sapphire femtosecond oscillator. The supercontinuum is used as a multi-spectral excitation light source in a two-photon excited fluorescence microscope. We demonstrate that three-color fluorescence images of organelles in a cell can be simultaneously acquired.