The infrared spectra of 75 samples of 15 rapeseed varieties were obtained by means of Fourier transform infrared (FTIR) spectroscopy technique. The results show that the infrared spectra of the samples are very similar. By the spectral professional software Omnic8.0, two spectral databases were constructed. Lib01 includes the average spectra of 9 samples from Yunnan, while Lib02 is constructed from the average spectra of all 15 varieties. The correlation search and the squared differential difference retrieval of the spectra of Yunnan samples were performed with the spectral database Lib01 in full spectrum range, respectively. The obtained matching values reflect that the samples have the closest correlation with each other only within the same species, with the correct rate of 77.8% for the correlation search, and that of 82.2% for the latter. The squared differential difference retrieval for the 15 sample spectra was carried out with Lib02 in full spectral range and in the specified range of 1 700～950 cm-1, yielding correct rate of 82.7% and 90.6% respectively. These results show that FTIR combined with the spectral retrieval method can identify the different varieties of rapeseed, and the squared differential difference retrieval in the specified spectral range is a more effective and simple way for distinguishing different varieties of rapeseed.