In the presented study, Central European Corydalis species, namely C. cava, C. intermedia, C. pumila, and C. solida were investigated by nonaqueous capillary electrophoresis-electrospray ion trap mass spectrometry (NACE-ESI-MS) utilizing an electrolyte consisting of 50 mM ammonium acetate, 1 M acetic acid and 10% methanol in acetonitrile, applying a separation voltage of 30 and 20 kV for 1 s for injection. Isopropanol-water (1:1) was used as sheath liquid at a flow-rate of 3 microl/min. Peak assignment was assisted by multistage-ESI-mass spectrometry (ESI-MSn). The optimized method was fully validated (RSD inter- and intraday < 5%, LOD < 2.3 microg/ml, LOQ < 27.6 microg/ml, recovery rates > 98.8%) and subsequently applied for the qualitative and quantitative determination of isoquinoline alkaloids in single plant tubers (sample size < 0.5 g) of the four Central European Corydalis species, each of them showing a characteristic and unique alkaloid pattern. Application of a principal component analysis (PCA) to the complete dataset of 39 analytes and 79 samples allowed the identification of 8 analytes responsible for lot discrimination. Hierarchical cluster analysis and descriptive statistical methods were used to confirm the findings of the explorative PCA.