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Background and Objective: Isolation of yeasts and keeping them for use in the food and drug industries need rapid and precise methods. Traditional methods of identification of yeasts and fungi have many defects, and new molecular methods, despite their widespread application and high efficiency, are expensive and not appropriate for routine use. The aim of this study was to find a simple and rapid method for yeast identification. Materials and Methods: Seven yeast strains, including two standard zero-caloric-sweetener-producing strains, two non-producing strains and three strains naturally producing non-caloric-sweeteners were examined in order to compare efficiency of FT-IR and molecular technique in yeast identification. Results: This study showed that similar and dissimilar yeast species (as regards species and genera) have identical and different spectrua, respectively. Quantitative evaluation of the yeast strains was performed using curve fittings of the polysaccharide, protein, and fatty acids regions. Conclusion: Based on the findings, it can be concluded that FT-IR is a fast and effective method for identification of yeast strains. The advantages of this new method are simplicity of sample preparation, short analysis time, and high validity. Keywords: FT-IR, Low-calorie sweetener, Ribosomal RNA, Yeasts