A combined method of high performance liquid chromatograph-elecrtrospray-ionization mass spectrometer(HPLC-ESI-MS/MS) coupled with a photodiode array detector(HPLC-DAD) and principal component analysis(PCA) was applied to the qualitative and quantitative analyses of alkaloids in Cortex Phellodendri(CP) samples, and to the differentiation of two species of CP, Cortex Phellodendri Chinensis(CPC) and Cortex Phellodendri Amurensis(CPA). Twenty-two peaks appeared in the HPLC-MS base peak chromatogram of CP detected by the HPLC-ESI-MS/MS analysis, and the alkaloids were identified according to the MSn data, the known MS fragmentation rules and the literature data. Five alkaloids including berberine, palmatine, jatrorrhizine, phellodendrine and magnoflorine were simultaneously determinated by the HPLC-DAD. Berberine was the primary component in all CP samples, and the contents of berberine and palmatine were exploited to be two critical parameters for effective discrimination between the two species of CP. The average content of berberine in CPC(58.75 mg/g) was higher than that in CPA(9.16 mg/g), while the content of palmatine was less, only 0.25 mg/g in CPC and 4.19 mg/g in CPA. With the use of PCA, samples datasets were separated successfully into two different clusters corresponding to the two species, and berberine, palmatine, phellodendrine and magnoflorine contribute most to the above mentioned calssifying. The proposed method proved to be a useful tool in the quality control of Chinese herbal medicines. A combined method of high performance liquid chromatograph-elecrtrospray-ionization mass spectrometer (HPLC-ESI-MS / MS) coupled with a photodiode array detector (HPLC-DAD) and principal component analysis (PCA) was applied to the qualitative and quantitative analyzes alkaloids in Cortex Phellodendri (CP) samples, and to the differentiation of two species of CP, Cortex Phellodendri Chinensis (CPC) and Cortex Phellodendri Amurensis (CPA). Twenty-two peaks appeared in the HPLC-MS base peak chromatogram of CP detected by the HPLC-ESI-MS / MS analysis, and the alkaloids were identified according to the MSn data, the known MS fragmentation rules and the literature data. Five alkaloids including berberine, palmatine, jatrorrhizine, phellodendrine and magnoflorine were simultaneously determinated by the HPLC- DAD. Berberine was the primary component in all CP samples, and the contents of berberine and palmatine were exploited to be two critical parameters for effective discrimination between the two species of CP. The average content of berberine in CPC (58.75 mg / g) was higher than that in CPA (9.16 mg / g) while the content of palmatine was less, only 0.25 mg / g in CPC and 4.19 mg / g in CPA. With the use of PCA, samples datasets were separated successfully into two different clusters corresponding to the two species, and berberine, palmatine, phellodendrine and magnoflorine contribute most to the mentioned mentioned calssifying. The proposed method proved to be a useful tool in the quality control of Chinese herbal medicines.