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Femtosecond-laser ionization mass spectrometry (fs-LIMS) is demonstrated to be a powerful analytical method providing access to the qualitative distinction of structural isomers of ortho-, meta-, and para-fluorotoluene. The key point of the approach presented is a systematic variation of the spectral phase of the fs-laser pulses, which characteristically affects the fragmentation pattern observed in the mass spectra. Variation of the linear chirp parameter is also helpful for rationalizing the fragmentation mechanism. Ultimately two ternary mixtures of the