Fourier transform infrared (FTIR) spectroscopy was used to study two kinds of broad beans with white and green cotyledons respectively. The results show that the infrared spectra of the two kinds of broad beans are similar and mainly made up of the absorption bands of protein, and polysaccharides. The second derivative infrared spectra amplified the differences and revealed that there were some obvious differences in the range of 1 800-700cm-1 and 1 200-700cm-1. Hierarchical cluster analysis (HCA) were used for the discrimination of the two kinds broad beans based on the second derivative spectral data in the region of 1 611-1 100cm-1, and yielded 88.9 % accuracy. The spectra in the range from 1700 to 1600cm-1 were used to perform Fourier self-deconvolution and curve fitting, which obtained nine peaks. The ratios of relative areas of the bands at α-helix, β-sheet, β-turn and the unordered structure of protein in white beans were 67.71%, 35.6%, 35.6% and 21.09% respectively, while the ratios in green beans were 8.02%, 31.59%, 37.12% and 23.27% respectively. The results indicate that the secondary structure of protein was different in the two kinds of broad beans.