Near-infrared (NIR) spectroscopy and Fourier-transform infrared (FT-IR) spectroscopy were applied for the discrimination of genomic DNAs from different genotypes of plants. From the results of NIR and FT-IR analyses for the detection of genetically modified (GM) maize, GM and non-GM maize genotypes were distinguished based on the absorbance wavelength or wave number. Statistical analysis of the data obtained suggested that FT-IR gave clearer and more reproducible results than NIR for the discrimination of a GM maize line from a non-GM one. Based on these findings, FT-IR was used to discriminate much smaller variation such as allelic differences at one locus in isogenic lines of rice, and was also applied to the characterization of higher levels of genomic variation using typical indica and japonica rice varieties. In the case of isogenic lines, no obvious difference was observed. On the other hand, indica and japonica varieties could be clearly distinguished, and two varieties belonging to the indica varietal group could also be separated. It was concluded that this method may enable to discriminate among different varieties, and could become an easy and effective method of plant genotyping.