In the present study we examined the potential of Fourier Transformed Infrared (FTIR) spectroscopy for accurate identification and differentiation of mixed bacteria samples in a time span of a few minutes. The bacterial samples used in this study are Escherichia (E.) coli, Bacillus (B.) megaterium and a mixture of E. coli and B. megaterium. The best results of differentiation were obtained within the 675-1800 cm-1 range. In this range the dimension of the feature vector is 293. Principal components analysis (PCA) followed by linear discriminant analysis (LDA) as a linear classifier were performed on the spectra of the three measured classes. When differentiating between the pure sets of E. coli and B. megaterium, 100% success was obtained for a feature vector composed of the first 12 principal components (PCs). An error rate of less than 2% was achieved taking only the first 20 PCs among the three categories of samples.