Mycorrhizal fungi are responsible for providing an array of benefits for both their mutualistic plant hosts and their surrounding ecosystems. In addition to the acquisition of water and nutrients - most notably nitrogen and phosphorus – for their host plants, mycorrhizal fungi provide both a physical barrier to pathogens and regulate systemic gene expression in planta with effectors and other small secreted proteins. In ecosystems, mycorrhizal fungi contribute to nutrient cycling and may possess novel enzymes for the breakdown of a wide array of natural and synthetic chemicals. In an effort to better understand the molecular mechanisms underpinning the mycorrhizal association, more than 30 model mycorrhizal fungal taxa are being investigated at the genome level. To be compared with saprophytic fungal taxa and using the Laccaria bicolor and Tuber melanosporum genomes as disparate models for independently derived mycorrhizal associates, all fungi are currently undergoing genome and transcriptome sequencing using the 454 FLX Titanium and Illumina GA platforms at the Joint Genome Institute of the U.S. Department of Energy. Preliminary analyses show the presence of highly conserved regions syntenous to Linkage Group I of L. bicolor across fungi in the Agaricales, as well as proliferation of transposable elements resulting in variation in genome size.