Plants with bioactive specialized metabolites, also referred to as medicinal plants, have been used by human, and other primates for thousands of years. These bioactive compounds are known to affect humans and cultures cells in many ways including but not limited to anti-viral, anti-oxidant, anti-depressant, anti-cancer, anti-bacteria, and anti-fungal. The accumulation levels of these compounds inside the plant are highly influenced by genotype, and by biotic and abiotic cues. Because of the importance of these compounds in pharmaceutical production, I worked to understand the metabolism of acylphloroglucinols, dianthrones, and flavonoids produced in Hypericum gentianoides and H. perforatum. To accomplish this goal, this research consisted of several components: identify previously unknown acylphloroglucinols and their predicted intermediates to establish a acylphloroglucinol biosynthetic pathway by using MS techniques in H. gentianoides, identify where acylphloroglucinols and acylphloroglucinol intermediates accumulate in H. gentianoides by using MS techniques, identify putative biosynthetic genes by using methods to correlate metabolite shifts to shifts in transcripts, validate polyketide biosynthetic genes with in vitro expression studies in E. coli