There are over 1.5 Million fungal species and they play critical role in shaping Earth ecosystems. Better understanding of pathogens and symbionts is critical for a sustainable growth of plants. Fungi are the most efficient degraders of plant biomass to convert it into bioenergy. Many other new metabolic processes and enzymes are encoded in fungal genomes. Fungal genomics may offer answers to critical challenges of future such as food, medicine, energy and the environment. This talk will describe approaches used in large scale genomics- to explore phylogenetic and ecological diversity of fungi. It will also illustrated how genomic data can improve our understanding of plant-fungal interactions and enable practical applications for energy and the environment.