Herba Cistanche (Rou Cong Rong in Chinese), dried succulent stems of Cistanche deserticola or C. tubulosa, is a famous Chinese herbal medicine and has been recorded in the Chinese Pharmacopoeia. In recent years, another two non-official species, C. salsa and C. sinensis have also been used as Herba Cistanche in some regions of China. To investigate the possibility of using these two non-official species as alternatives to the official species, a high-performance liquid chromatography-diode array detection-mass spectrometry (HPLC-DAD-MS) fingerprint method was developed to comparatively analyze the crude herbs of these four species. The fingerprint of C. deserticola, a historically certified species of Herba Cistanche, serves as 'standard pattern' for comparing the similarities with the other species by means of similarity and Principle Component Analysis. Additionally, 18 characteristic peaks in the fingerprints were identified by comparing their retention times, UV spectra and ESI-MS data with those of the reference substances and/or the data in the literatures. The comparative results demonstrate that the fingerprints of C. tubulosa and C. salsa possess high similarity to the standard pattern, suggesting that these two species may be used as alternative species; while that of C. sinensis has low similarity (0.053 correlation coefficient) to the standard pattern, indicating that it cannot be used as the substitute of the official herb. However, the varying fingerprint patterns among the samples of C. deserticola collected from various habitats illustrate that the quality consistency of crude herbs is still a problem worthy of serious concern.