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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 te