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<i>Trichophyton indotineae</i> is an emerging pathogen which recently spread from India to Europe and that is more prone than other species of the <i>Trichophyton mentagrophytes</i> complex to show resistance to terbinafine, resulting in the necessity of rapid identification. Here, we improved the online MSI-2 MALDI-TOF identification tool in order to identify <i>T. indotineae</i>. By multiplying the culture conditions (2 culture media and 6 stages of growth) prior to protein extractions for both test isolates and reference strains, we added 142 references corresponding to 12 strains inside the <i>T. mentagrophytes</i> complex in the online MSI-2 database, of which 3 are <i>T. indotineae</i> strains. The resulting database was tested with 1566 spectra of 67 isolates from the <i>T. mentagrophytes</i> complex, including 16 <i>T. indotineae</i> isolates. Using the newly improved MSI-2 database, we increased the identification rate of <i>T. indotineae</i> from 5% to 96%, with a sensitivity of 99.6%. We also identified specific peaks (6834/6845 daltons and 10,634/10,680 daltons) allowing for the distinction of <i>T. indotineae</i> from the other species of the complex. Our improved version of the MSI-2 application allows for the identification of <i>T. indotineae</i>. This will improve the epidemiological knowledge of the spread of this species throughout the world and will help to improve patient care.