Forty-five Bacillus isolates were obtained from different foods (spices, grains, dried milk), the isolates were identified using traditional method from Bergey's manual based on morphological tests (gram staining, spores staining), physiological tests (optimum growth temperature, pH, NaCl concentration) and biochemical tests (Voges-Proskauer, gelatin hydrolysis, esculin hydrolysis, β- Galactosidase test, Lysine decarboxylase and Ornithine decarboxylase, production of acid from different sugars). Bacterial suspensions were prepared from the isolates and FTIR spectrums were obtained using ATR unit, which consists of ZnSe prism, by scanning at the range of 4000-400 cm-1. Results revealed that the isolates represented 5 species of Bacillus (B. pumilus, B. subtilis, B. lentus, B. megaterium, B. cereus) and the potential of Fourier transform infrared spectroscopy-attenuated total reflectance (FTIR-ATR) method as a reliable method for discrimination among Bacillus isolates, which is accurate, rapid, easy to apply and cheap.