Fourier transform infrared spectroscopy (FT-IR) was applied for the first time for the discrimination of halophilic prokaryotes. In the current study, halophilic Bacteria and Archaea species were investigated according to their FT-IR profiles. Some of the halophilic isolates collected from ÇamaltÄ± Saltern in Turkey were also analyzed and their FT-IR profiles were compared with reference strains. Hierarchical cluster analysis was used to indicate discrimination. This study implies that FT-IR can be applied to discriminate species of Archae and Bacteria.