Therapeutic molecules from natural sources were identified mainly through conventional extraction/analysis procedure. In this study we used a PCR method to predict the presence of an end product in the metabolic pathway of flavone biosynthesis. Specific primers designed for chalcone synthase (CHS) (PCR control), 18S rRNA (template control) and flavone synthase (FNS) (target gene) were used to deduce the presence of flavones in the plants (Asparagus, Tea and different parts of lemon) studied. Results obtained by molecular method were comparable with the biochemical method. We propose that, this technique possesses great potential to be used with much sensitive realtime PCR to quantify minute amounts of secondary metabolites in unexplored plants and to foresee whether it is worthwhile to explore the possibilities of large scale extraction.