Rapid detection of biologically active natural products plays a key role in the phytochemical investigation of crude plant extracts. In order to perform an efficient screening of the extracts, both biological assays and HPLC analysis with various detection methods are used. Techniques such as HPLC coupled to UV photodiode array detection (LC/DAD-UV) and to mass spectrometry (LC/MS or LC/MS/MS) provide numerous on-line structural data on the metabolites prior to isolation. The recent introduction of HPLC coupled to nuclear magnetic resonance (LC/NMR) represents a powerful complement to LC/UV/MS screening. Various plant species belonging to the Gentianaceae and Leguminosae have been analysed by LC/UV, LC/MS, LC/MS/MS and LC/NMR. These hyphenated techniques allow a rapid structural determination of known plant constituents with only a minute amount of plant material. Simple bioautographic assays such as those used for screening antifungal constituents can also be performed on-line directly by collecting HPLC peaks and measuring the activity against the fungi of interest. These bioassays permit a rapid localisation of the bioactive natural products. With such a combined approach, the time consuming isolation of common natural products is avoided and an efficient targeted isolation of compounds presenting interesting spectroscopical or biological features is performed. Several representative applications of the use of LC/Ms and LC/NMR for the dereplication and identification of antifungal constituents are presented in the present paper.