Fourier transform infrared (FTIR) spectroscopy, in combination with multi-variate statistics, has been a novel tool to identify and classify microorganisms in recent years. In the present study, Fourier transform infrared spectroscopy was used to identify Fusarium belonging to F. oxysporum, F. moniliforme, F. graminearum, F. semitectum, and F. rnvale . Distinct spectral differences among these strains were observed from their high-resolution and well-reproducibility infrared spectra in the frequency regions of 3000-2800 cm-1, 1800-1600 cm-1, and fingerprint region. According to the characteristic bands in these regions, different Fusarium species could be identified. And identification by hierarchical cluster analysis was more scientific and reasonable and it also presented a degree of comparability among these strains. But the result was not becoming on reflecting the characteristic of cladistics. FTIR shows high potential as a rapid, accurate and easy-to-use method for the identification of microorganisms. It will be an important tool in microbiological studies.