Huangbai (cortex Phellodendri, the dried bark of Phellodendron amurense or Phellodendron chinense) is one of the important traditional Chinese medicines. Protoberberine alkaloids were reported to contribute to the biological activity of this species. A highly specific and sensitive method using (1)H NMR has been developed for the quantitative determination of protoberberine alkaloids in Phellodendron species and their commercial traditional Chinese medicine prescriptions. In the region of delta 8.6-8.9, the signals of H-13 of berberine (1) and palmatine (2), were well separated from other signals in methanol-d(4). The quantity of the compounds was calculated by the relative ratio of the integral values of the target peak of each compound to the known amount of internal standard anthracene. This method allows rapid and simple quantization of protoberberine alkaloids from Phellodendron species or the more complex commercial prescriptions in 5 min without any pre-purification steps. The recoveries of berberine and palmatine from P. amurense were in the range of 95-106%. Limit of detection (LOD) and limit of quantitation (LOQ) of them were 1.0 and 1.8 microg/mL, respectively. The advantages of the method were that no reference compounds are required for calibration curves, the quantification could be directly realized on a crude extract, the better selectivity for protoberberine alkaloids and a very significant time-gain could be achieved, in comparison to conventional HPLC methods, for instance.