This thesis aims at investigating novel and rational strategies to identify secondary metabolites from plant or microbial origin by targeted isolation; either guided by HPLC-bioactivity profiling or by metabolomics. Firstly, a microfractionation strategy was elaborated for mass-limited extracts that is compatible with the detection and identification of the purified compounds by microflow NMR as well as in vivo zebrafish bioassays. This approach revealed several flavanoids that explain the antiangiogenic activity of the Rhynchosia viscosa extract. Secondly, strategies were developed for the analysis of microorganism co-cultures. Microfractionation led to the isolation of a co-culture induced compound in the low microgram range from the co-culture of Acremonium strictum and Fusarium oxysporum. For the co-culture of Hohenbuehelia reniformis and Fusarium solani, multivariate data analysis highlighted metabolites responsible for the differences between pure culture and co-culture extracts. A two-step chromatographic purification permitted the targeted isolation of highlighted metabolites – u.a. several novel and anti-Fusarium quinones.