Cellulose is the major component of plant biomass, and microbial cellulose utilization is a key step in the decomposition of plant detritus. Despite this, comparatively little is known about the diversity, size and activity of cellulolytic microbial communities in soil. Fungi are well-known for their cellulolytic activity, and fungi are believed to be key organisms in the decomposition of plant litter material in most terrestrial ecosystems. We developed new sets of oligonucleotide primers for fungal exo-cellulales (cellobiohydrolase, cbhI) and used these to isolate an approximately 600 base-pair gene fragment from several common litter-decomposing Basidiomycete and a wood-decaying Ascomycete. Cloning of the fragments revealed multiple allelic forms of distinct cbhI genes in these species. We also isolated and cloned cbhI genes from the forest floor and mineral soil of two upland forests in northern Michigan, one composed of oak and the other composed of sugar maple. BLAST-P and phylogenetic analysis revealed that the lignin-rich oak ecosystem was dominated by a low-diversity of predominantly Basidiomycete cbhI genes, whereas the cellulolytic community of the lignin-poor maple ecosystem was more genetically diverse. Quantitative PCR (qPCR) of the cbhI gene demonstrated that the forest floor of the oak ecosystem harbored 1000 times more cbhI copies/g than the underlying mineral soil (~10^9 vs 10^6). In contrast, cbhI copies/g were both lower (~10^7) and more equally distributed in the forest floor and mineral soil of the maple ecosystem. Our results represent a first step towards unlocking the identity and dynamics of the cellulolytic fungal community in situ.