Rationale: Fangchi (F.) species from four different origins have been widely used to treat or prevent diseases, and their main constitutes are several types of alkaloids. Identification of alkaloids in F. species is a necessary step to understand the therapeutic properties of each different origin, but this has not yet been fully performed. Methods: Several types of alkaloids were extracted from F. species using ultrasonication with 70% CH3OH and the extract was partitioned at pH 2 and 12 to enrich alkaloid constituents and to remove interferences. The separation of alkaloids in the Fangchi extract was performed on a C18 column using gradient elution and their tandem mass spectra were obtained by quadrupole time-of-flight tandem mass spectrometry (QTOF-MS/MS) to perform accurate mass measurements of fragment ions for the alkaloid constituents. Results: Several types of alkaloids were successfully separated and identified by LC/ESI-MS/MS. The structural assignment of individual alkaloids was performed based on convergence of MS/MS spectral data, pH partitioning behavior, LC retention behavior, and accurate mass measurements. The pH partition of the extract provided structural information about unknown alkaloids extracted from Fangchi species. A total of 28 compounds were identified and tentatively characterized, and of these 10 alkaloids were reported for the first time in the investigated F. species. Conclusions: The chemical profiling of alkaloids in F. species with different origins was performed for the first time and provided diagnostic ions for diverse alkaloids in F. species. Marker compounds were suggested based on the 28 characterized compounds for quality evaluation and the differentiation of Fangchi species with four different origins. Copyright © 2015 John Wiley & Sons, Ltd.