Fungi are the main organisms responsible for plant biomass degradation in soils. While many studies have evaluated the impact of tree species on the taxonomic diversity of soil fungi, very few of them have addressed their functional gene diversity. In the present study, we assessed the impact of tree species, differing with respect to litter quality, and sampling dates on the diversity of four expressed fungal gene families: one housekeeping gene used as taxonomic marker and three others encoding key enzymes implicated in lignocellulose degradation selected as functional markers. This was performed by the high throughput sequencing of gene-fragments amplified from forest soil mRNA using fungal specific primers. Messenger RNAs were extracted from 10 soil samples collected over two seasons in plots planted with either the conifer Picea abies or the angiosperm Fagus sylvatica in a common garden experiment. Independently of the gene-family, less than 20% of the fungal transcripts were identified in both forest types. For all four fungal gene-families, variance partitioning identified the tree species and its interaction with the sampling plot as the factors that contributed most to global gene diversity (between 29% and 32%), while the sampling dates accounted for less than 9%. Further analysis of the contribution of soil proprieties revealed that the tree species-generated C/N ratio is the most important factor driving functional gene distribution (between 6% and 29% of the variation explained). Similarly, for each fungal gene family, statistical analyses identified tree species as the main factor responsible for variations in similarity between samples (as estimated by the Bray-Curtis beta diversity index). These results highlight that tree species, differing with respect to litter quality, selected different soil fungal communities expressing different set of genes involved in plant organic matter degradation.