Fourier transform infrared (FTIR) spectroscopy is considered to be a rapid, reliable, sensitive, and a cost-effective technique, which could be used as an efficient tool for microorganism identification. Since bio-molecules, such as lipids, carbohydrates, and nucleic acids, have their own unique ‘vibrational’ fingerprints and characteristic functional groups, which correspond to specific infrared light frequencies, FTIR spectrum obtained for any compound gives the information on the unique ‘fingerprint’. The objective of this study was to investigate the ability of FTIR spectroscopy for differentiating different species of filamentous fungi. In this study, Erkence cultivar olives which were collected from different orchards were used for different fungal strain isolation. The fungi isolates were grown on Malt Extract Agar (MEA) and Czapek Yeast Agar (CYA) at room temperature of 25ºC for 10 days. 15 different genera and 53 species were identified by using Polymerase Chain Reaction (PCR) and characterized in terms of DNA sequencing. FTIR spectroscopy was applied to 71 species as a novel technique to identify fungi. 18 pre-defined species that were collected fom previous studies, were also used for FTIR spectroscopy investigation. Statistical analysis of the data was performed by using a principal component analysis (PCA). FTIR spectroscopy provides a potentially powerful approach to differentiate filamentous fungi.