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An encryption algorithm for hyperspectral data in fractional Fourier domain is designed. Firstly, the original hyperspectral image is separated into single bands and then each pair of bands are regarded as the real and imaginary part of a complex function by using an affine transform. Subsequently, the complex functions are encoded and transformed in fractional Fourier domain (FrFT). The parameters in affine transform and FrFT serve as the key of the encryption system. The proposed encryption scheme can not only protect the image information in spatial domains but also the spectrum information in spectral domains. Various experiments are given to demonstrate the validity and capability of the proposed encryption scheme.