The on-line separation and identification of two important taxonomic markers for plant species of the Paepalanthus genus, the flavonoids 6-methoxykaempferol-3-O-beta-D-glucopyranoside and 6-methoxykaempferol-3-O-beta-D-6"(p-coumaroyl)glucopyranoside, has been performed with an HPLC-NMR coupling using C30 phase. 1D spectra have been recorded in the stopped-flow mode for the two predominant chromatographic peaks. This is the first application of HPLC-NMR coupling using C30 phase to a taxonomic problem. The technique drastically reduces the required amount of sampling for structure determination.