TS2 sequences and high-performance liquid chromatography (HPLC) fingerprint method were established to provide reference for the quality control of F. pandurata. MEGA6.0 was used to analyse ITS2 sequences,calculate K2P genetic distances,construct neighbor joining (NJ) phylogenetic tree.Secondary structure was analyzed by online ITS2 database.HPLC was used to establish the fingerprint and determine the content of psoralen and bergapten.The length of ITS2 sequence from F. pandurata is 210 BP and the average GC content is 62.37%.The length of ITS2 sequence of the related species ranged from 218 to 232 BP,and the content of GC ranged from 60.25% to 64.03%.The average genetic distance of K2P from F. pandurata was less than the interspecific genetic distance between F. pandurata and its related species.NJ tree showed that ITS2 could distinguish F. pandurata and its related species,and there were significant differences in the number of arms,arm length,number of stem rings on arms and the angle between arms in ITS2 secondary structure.The similarity of HPLC fingerprints from F. pandurata in different habitats ranged from 0.902-0.981 and the data showed 10 common peaks.Peak 8 was identified as psoralen,peak 9 was bergapten,and the content of psoralen was 1.01-4.80 mg/g,bergapten was 0.96-4.88 mg/g.The similarity of the common pattern between the related species and F. pandurata was less than 0.807.The content of psoralen in F. pandurata var.holophylla,F. pandurata var. angustifolia,and F. hirta was 0.38-0.63,1.08-1.32,2.45-14.73 mg/g,respectively.The content of bergapten in F. pandurata var. angustifolia was 0.25-0.34,and F. hirta was 0.13-0.74 mg/g.The content of bergapten was not detected in F. pandurata var. holophylla.The results showed that ITS2 sequences and HPLC fingerprint can be used for identification of F. pandurata and its related species.The established HPLC fingerprint analysis method is simple,specificity and reproducibility,which provides a reference for the quality evaluation of F. pandurata.