Nigella glandulifera Freyn et Sint seeds (NG) as well as Nigella sativa L. seeds (NS) have been employed as folk remedies for centuries. However, little work has been done on their quality control. In order to assess the quality and guarantee therapeutic effects, the chemical constituents of the two herbs were extensively characterized by ultra-performance liquid chromatography coupled with electrospray time-of-flight mass spectrometry (UPLC-Q-TOF/MS), and a simple, practical, and reliable HPLC fingerprinting method was established and applied to determination of 20 batches of samples. With their chromatographic fingerprints, the two species were successfully differentiated by pattern recognition methods, namely, principal component analysis (PCA) and partial least square discriminant analysis (PLS-DA). Results from this study show that the proposed analytical methods can be applied to the quality control of the seeds and have high potential to ensure their safety and efficacy.