Purpose of Review: The continued, rapid development of novel molecular genetic tools is contributing to a better understanding of forest-associated fungi and their interactive roles within diverse forest ecosystems. This paper focuses on recent developments of DNA-based diagnostics/detection, phylogenetics, population genetics, genomics, and metagenomics tools that have been applied to forest-associated fungi to better understand their roles in forest ecosystems and provide key insights for managing forest health. Recent Findings: With the advent of new molecular technologies, we can better understand the biology of forest fungi by examining their genetic code. By utilizing genomics, fungal pathogens’ biological functions can be deduced from its genomic content. Further, high-resolution marker systems allow the determination of a pathogen’s population genetics and genomics, which provides important insights into its global movement and genetic shifts in local pathogen populations. Such genetic information has diverse applications for forest management to improve forest health. Lastly, new technologies in metagenomics will enhance the abilities to detect, describe, and utilize the complex interactions among fungal pathogens/symbionts, host trees, and associated microbial communities to develop novel management strategies for forest ecosystems. Summary: Continued development and applications of molecular genetic and genomic tools provide insights into the diverse roles of forest-associated fungi in forest ecosystems, but long-term, wide-scale research is needed to determine how ecological functions are influenced by complex ecological interactions among microbial communities, other forest ecosystem components, and the environment. Such approaches may foster a paradigm shift away from single microbial pathogens, decomposers, or symbionts interacting with a single host or substrate, and provide more holistic approaches toward understanding interactions among microbial communities that drive forest health processes.