In the present paper, Fourier transform infrared spectroscopy (FTIR) associated with second derivative infrared spectroscopy and two-dimensional correlation spectroscopy (2D-IR) were used to analyze the 3 different sources of Hebra cistanche. The results showed that these IR spectra showed their different macro-fingerprint features: the charactersistic peaks of C. deserticola were located at ~1 730, 1 633, 1 156, 1 081, 1 025 and 931 cm-1 and those of C. tubulosa were at 1 692, 1 631, 1 604, 1 516, 1 265 and 1 023 cm-1, respectively. The only two peaks at ~1 151 and 1 085 cm-1 of C. salsa were different from that of C. deserticola. As a result, the IR spectrum of C. deserticola could be identified obviously from that of the C. tubulosa, whose similar index was only 0.623 3, but it was very similar to that of C. salsa, whose similar index was up to 0.904 8, demonstrating very similar ingredients. However, the difference between C. deserticola and C. salsa was obvious in the second derivative IR spectra: the shape of the two peaks of C. deserticola at ~1 730 and 816 cm-1 were much sharper. In addition, the fingerprint characters in 2D-IR spectra were more visualized. The three kinds of herbs were quite different from each other in the number and intensity of autopeaks. Therefore, FTIR macro-fingerprint method can identify different sources of Hebra cistance fast, nondestructively and effectively.C. deserticola; C. tubulosa; C. salsa; Identification