Fungi are tremendously diverse and play wide-ranging roles in forest ecosystems. Interactions between fungi and woody roots are involved in important processes including wood decay, root disease, and symbiotic relationships. In addition, some fungi feed on other fungi, acting as natural regulators of fungal populations. Identification of the diverse fungi isolated from wood can be difficult and tedious. Identification in the past has been based on morphology (physical form and structure), ecology (adaptation to particular niches), and pathology (disease symptoms and target host). Challenges to identifying fungi include the fact that many species that grow in wood will not grow under laboratory conditions, and many of those that do grow will not produce fruiting bodies necessary for identification. Currently, DNA analysis is being used to identify fungi and examine relationships among fungal groups. DNA fragments are analyzed by comparing differences in sequences. Sequence analysis provides valuable insight into evolutionary history both for broad relationships at family, order, and class level, and also to resolve relationships among or within species. Several databases contain extensive data on fungi. Unknown organisms can usually be identified to the species or species group by comparing DNA information with information in the databases. A recent study (Hoff 2002) used DNA sequencing combined with morphological verification to examine fungi found in woody roots of Douglas-fir and ponderosa pine. An unexpected finding was that the two predominant groups of isolated fungi corresponded to 1) a genus of heat-resistant fungi that may be active in bioprotection, and 2) a genus of common soil fungus not previously detected in living roots. The implications for fire and host succession effects on disease through these or other previously overlooked fungi are of great interest. The diversity of fungi occupying ecological niches on and in woody roots of forest trees is largely unexplored. Future studies will determine if management practices such as prescribed burning could be used to favor beneficial fungi that are heat resistant, while discriminating against fungal pathogens that are less heat tolerant. As the role of fungi is better understood, information should become available to improve sustainable forest practices.