Viticis Fructus is the dried ripe fruit of Vitex trifolia L. (VTF) or V. trifolia subsp. litoralis Steenis (VTLF). Different botanical sources of the same herbal medicines may have different clinical efficacies, but few studies have reported the comparative identification of VTF and VTLF.To establish a high-performance liquid chromatography (HPLC) method for the simultaneous assay of 11 constituents in Viticis Fructus, to compare the chemical compositions of VTF and VTLF, and to identify chemical markers for the discrimination and quality evaluation of the two botanical origins of Viticis Fructus.An HPLC-diode array detection (DAD)-high-resolution mass spectrometry (HRMS) method was developed for the simultaneous separation and quantification of 11 constituents in 21 batches of Viticis Fructus samples from different sources in China. Moreover, chemometrics were performed to compare and discriminate VTF and VTLF samples.The results from 11 batches of VTF and 10 batches of VTLF were compared for 11 components, of which 3,4-dicaffeoylquinic acid and 3,5-dicaffeoylquinic acid were identified and quantified in Viticis Fructus for the first time. The quantitative analysis showed significantly higher chlorogenic acid and casticin contents in VTLF than in VTF, and the chemometric analysis indicated that chlorogenic acid and casticin were responsible for the significant differences between VTF and VTLF; these two compounds might be used as chemical markers to distinguish the two original plant sources of Viticis Fructus.The present work provides useful information for understanding the chemical differences between VTF and VTLF. This work also provides feasible methods for the quality evaluation and discrimination of herbal medicines originating from multiple botanical sources.