Fungi are a rich source of bioactive small molecules. However, the large number of secondary metabolite (SM) biosynthetic gene clusters (BGCs) encoding these molecules in their genomes suggests their biosynthetic potential is far greater than we previously appreciated. The mining of fungal genomes therefore holds great promise for the discovery of new chemical entities for pharmaceutical and agricultural applications. As more and more fungal genomes become available, the accompanying number of BGCs is quickly becoming unmanageable. Along with improving molecular genetic tools to accelerate the translation of BGCs to small molecules, we must devise strategies to prioritise BGCs most likely to encode the biosynthesis of novel small molecules and molecules with new or improved bioactivities or functions. Here, we will discuss our strategies and successful examples of using genomics and synthetic biology to facilitate the discovery of bioactive compounds. This includes the discovery of phytotoxic compounds from plant pathogens and antimicrobial compounds.