Fungi have long been a prolific source of clinically approved drugs. The antibiotic penicillin, the cholesterol lowering statins, and the immunosuppressant cyclosporine have changed the treatment of human diseases in the last century. Recently, genome analysis of filamentous fungi has revealed that the biosynthetic potential for natural product expression is far greater than what is traditionally observed in laboratory culture. To this end, strategies to induce the expression of these otherwise transcriptionally silent natural product gene clusters are key to the continued discovery of chemical diversity. The research presented includes four manuscripts on gene activation strategies in fungi, with foci including ecological, chemical, and genetic approaches. Knockout of an epigenetic regulator in Fusarium graminearum resulted in the identification of two novel terpenes (tricinolonoic acid and tricinolone) and one novel polyketide (protofusarin). Furthermore, bioinformatics analysis allowed for the identification of the gene clusters responsible for the production of tricin terpenes and gibepyrones. In Chalara sp. 6661, treatment with the HDAC inhibitor vorinostat resulted in the production of four novel xanthones (chalanilines A-B and two xanthone-adenosine derivatives). Synthesis of isotopically labeled vorinostat and consequent feeding studies confirmed that chalanilines A and B were biotransformation products of vorinostat. A nutrient manipulation study in Aspergillius terreus showed selective production of metabolites via LCMS based metabolomics and enabled the discovery of new compounds including 7-desmethyl citreoviridin. Co-cultivation of two developmental forms of Aspergillius alliaceus resulted in the expression of novel, cytotoxic, bianthrone polyketides (allianthrones A-C). In each instance presented, application of a gene activation technique elicited the production of previously undescribed natural products.