The Fungal Environmental Sampling and Informatics Network (FESIN; www.bio.utk.edu/fesin) is an NSF-funded network of mycologists and ecologists with a major goal of expanding the number of scientists who incorporate fungi into their studies. One of the barriers to inclusion of fungi in ecological research is the difficulty of identifying fungi from environmental samples. This full-day workshop will address the use of molecular tools for assessing fungal biodiversity. The workshop will target ecologists interested in working with fungi who have limited familiarity with molecular approaches. It will include presentations by leaders in the field and opportunities for discussion and informal interaction to promote collaboration. The morning session (introduction to methods) will include four topics, as well as a coffee break to encourage interaction: (1) Introduction to the major fungal lineages and the importance of considering phylogeny in studies of fungal ecology; (2) Sampling strategies and sample preparation; (3) Overview of molecular methods including nucleic acid extraction, amplification, T-RFLP, and cloning; (4) Nucleic acid sequence and T-RFLP acquisition, analysis and interpretation. The afternoon session (challenges and new technologies) will include sessions on: (1) Sampling issues particular to sample source (soil, plant tissues, spores, as well as culture-dependent and culture-independent approaches); (2) Selection of the spatial scale of sampling and the issue of hyperdiversity; (3) Emerging technologies and their uses, including RNA-based expression methods and analyses, massive parallel sequencing, metagenomics, and bioinformatics; (4) Conclusion and discussion.