To establish an HPLC fingerprint to evaluate the quality of Polygalae Radix, root xylem, and those collected in different growth ages or harvest time.Separation was performed at 30 °C on a Kromasil C18 column (4.6 mm x 250 mm, 5 μm); the mobile phases was acetonitrile and 0.05% H3PO4 water in the gradient elution; the flow rate was set at 1.0 mL · min(-1) and the detection wavelength at 314 nm; the quality discriminant analyses were accomplished by means of similarity analysis, cluster analysis, principal component analysis and neural network model.In 26 batches of Polygalae Radix, 24 batches fingerprint similarities were above 0.8. In 5 different growth or harvest time batches, 4 batches were above 0.8; in 8 batches root xylem samples, the similarities were all above 0.875. The similarity analysis was in accord with the quality discriminant analysis of cluster analysis, principal component analysis and neural network model.Fingerprint combined with chemical pattern recognition technique can effectively evaluate the quality of Polygalae Radix. The active substance species are all similar in cultivated, wild, different growth or harvest time Polygalae Radix and polygala root xylem, but the chromatography peak areas are different. The effective material contents are similar between wild and cultivated Polygalae Radix, but each chromatographic peak area of the root xylem is much smaller than that of Polygalae Radix. The chemical substance accumulation mainly depends on harvest month, but little growth time in Polygalae Radix.