Purpose: To develop an ultra-high performance liquid chromatography (UPLC) - photodiode array (PDA) method to compare the chemical composition of two different medicinal components of Pterocephalus hookeri. Methods: Samples were chromatographically separated in succession using Waters Acquity UPLCR BEH C18 column (2.1 × 100 mm, 1.7 µm) and gradient elution (0.2% phosphoric acid aqueous - acetonitrile). Using partial least squares discriminant analysis and one-way analysis of variance, attempts were made to distinguish different medicinal parts of P. hookeri. Results: Regression equation for 10 compounds showed good linear regression (R² > 0.9994). The relative standard deviations of precision, stability, repeatability and recovery were under 5%. Compared with the aerial plant part, the root had significantly higher levels of sylvestroside I (p < 0.01), cantleyoside (p < 0.001), dipsanosides B (p < 0.01) and dipsanosides A (p < 0.01), but significantly lower levels of loganic acid (p < 0.001), chlorogenic acid (p < 0.01), and isochlorogenic acid (p < 0.01). There were no significant differences between loganin, sweroside and isochlorogenic acid C. Conclusion: The described method is simple, accurate and reproducible, and can be used for the simultaneous determination of 10 major compounds of P. hookeri. The results demonstrate that there is variation in the chemical composition of the aerialpart and root of P. hookeri and that loganic acid and cantleyoside are the primary chemical biomarkers.