Fourier transform infrared spectroscopy (FTIR) combined with principal component analysis (PCA) and hierarchical cluster analysis (HCA) is used to study different kinds of capsicum frutescens L.. FTIR spectra of 50 samples are obtained from five species of capsicum frutescens L.. The results show that the infrared spectra of capsicum frutescens L. are similar, but tiny differences in wave-numbers and absorption intensities of peaks are observed in the range of 1800~800 cm-1. PCA and HCA are performed on the second derivative infrared spectra in this range. FTIR spectroscopy is found to be efficient in classification of capsicum frutescens L.. 50 samples are well divided into five groups and about 100% classification accuracy for HCA, about 98% accuracy for PCA are yielded. It is proved that FTIR combined with statistical analysis can be used to discriminate capsicum frutescens L..