Metarhizium fungi have dual lifestyles as insect pathogens and as rhizospheric plant symbionts. Since these fungi can vary widely in their virulence and host-specificity, they provide a powerful model for host-pathogen interactions. Today, it is clear the greatest potential of these fungi lies in their application as transgenic biotechnologies. Biotechnologies are rightly subjected to increased scrutiny, and this dissertation seeks to assess the risks and benefits of applying transgenic Metarhizium fungi using bioinformatics. After sequencing the early-diverged generalist Metarhizium frigidum, comparative genomics has upended our understanding of the trajectory of Metarhizium evolution. Using a functional gene microarray, I assessed the impacts these fungi have on the soil microbial community, establishing a protocol for evaluating possible risks of applying transgenic entomopathogenic fungi. To inform the evaluation and development of next-generation transgenic Metarhizium strains in the future, I evaluated the specific mosquito immune response to Metarhizium pingshaense during early infection with and without Plasmodium falciparum (the human malaria parasite) using transcriptomics. A strain of this fungus engineered to express a potent arthropod-derived, insect-specific neurotoxin in mosquito hemolymph, was also evaluated for mosquito control efficacy in semi-field trials in West Africa. Together, this body of work offers a comprehensive view of the evolution of this fungal genus and how transgenic fungi interact with insects, plants and microbes. The results herein comprise a framework for evaluating the risks and efficacy of transgenic fungi.