Fungi have long been used for discovery of new chemical scaffolds. In the clinical setting, the fungal natural products penicillin, statins, and cyclosporine have revolutionized medicine to treat diseases and infections. In the environment, fungal natural products have been used as herbicides, fungicides, and insecticides to protect crops, livestock, and commercial forests. As part of a broad survey of secondary metabolites produced by plant-associated fungi, the research presented includes three fungi from terrestrial and marine sources that were assessed for their chemical diversity. Chemical analysis let to the isolation of a new metabolite from Zasmidium pseudotsugae, an epiphytic fungus closely associated with Douglas-fir trees. From Penicillium crustosum, an algal-derived fungal endophyte, known metabolites were isolated and subjected to antimicrobial screening. Lastly, eight isolates of the wheat pathogen Fusarium graminearum exhibiting different in planta pathogenicity were subjected to comparative, metabolomic analysis. In each instance presented, fungi produced different molecules that can be used as tools to understand the chemical ecology of fungi.