Litter biochemistry and microbial community composition interact with atmospheric N deposition to influence soil C and N cycling. In an ongoing field study, experimental nitrate-deposition (80 kg nitrate-N ha-1 y-1) significantly reduced forest floor mass and soil organic C in a sugar maple-dominated forest, while phenol oxidase activity was increased. The opposite response occurred in a forest dominated by black and white oak. To determine the biological basis for these observations, we used culture-independent molecular methods to examine the fungal community responsible for the majority of lignin degradation in forest floor. The abundance of white-rot basidiomycetes was determined using a quantitative PCR assay targeting the phenol oxidase gene family. Quantity of phenol oxidase gene DNA was approximately 5-fold greater in oak forest floor than sugar maple forest floor, but was not significantly affected by N amendment. Phenol oxidase DNA explained a significant portion of the variability in phenol oxidase activity in oak litter, but not in sugar maple forest floor. Denaturing gradient gel electrophoresis (DGGE) of an amplified fragment of the ribosomal gene was used to examine general fungal community composition. Significant differences in fungal community composition were found between forest types, but experimental nitrate deposition had no effect on fungal community composition. We have demonstrated that abundance of the lignin-degrading fungi, and general fungal community composition, differ among forests, and this may create the basis for differences in response to N amendment between forest types.