The lack of specific fluorine detection at trace levels hampers the screening of microorganisms which can form novel fluorometabolites. So far only target analysis by ESI-MS using accurate mass and certain fragmentation or preconcentration and clean-up procedures has been used to perform 19F and 13C/1H NMR for the identification of novel fluorocompounds. Here we demonstrate that the analysis of complex media from microorganism cultures can be screened using a set of HPLC separations which are coupled parallel to CS-MAS as a fluorine specific detector and the ESI-MS as the molecular detection. This makes it possible to identify fluorine containing species without prior knowledge of the compounds and the use of clean up procedures. Here specifically we identify traces of a fluorometabolite (5′-fluoro-5′-deoxy-adenosine, 5′-FDA) in complex media of Streptomyces cattleya without preconcentration and target analysis.