On-line structure characterization of pyrrolizidine alkaloids in two various plant species (Onosma stellulatum W.K., family Boraginaceae and Emilia coccinea Sims., family Compositae) was performed by a newly elaborated RP-HPLC ion trap MS method with atmospheric pressure chemical ionization (APCI) interface. Different PAs (N-oxides, free bases, otonecine alkaloids) isolated were separated on Waters XTerra C18 column using a gradient elution. The combination of a CE-SPE with multiple isolation and fragmentation steps for specific masses in ion trap MS detector enabled fast and sensitive analysis of various types of PAs (N-oxides and free bases). In O. stellulatum, spectra 12 various types of structures (13 different alkaloids) have been determined for the first time: leptanthine-N-oxide, lycopsamine-N-oxide, heliospathuline, lycopsamine, trachelanthamine-N-oxide, dihydroechinatine, leptanthine, heliospathuline-N-oxide, 7-acetylintermedine, uplandicine, echimidine and echimidine-N-oxide. In E. coccinea, the following types of PAs were found: platyphylline-N-oxide, platyphylline (three stereoisomers with the same MS(n) spectrum), ligularidine, neoligularidine, neosenkirkine and also previously reported senkirkine. The method elaborated can be applied in the structural analysis of PAs in newly examined plant materials or food products but further analysis is needed to determine the stereochemistry in details.