Although a number of studies have indicated that microbes are key players in nutrient cycling, limitations on how to accurately assess their diversity have constrained further knowledge on the role of microbial diversity in organic matter decomposition in streams. Microbial diversity on leaf litter of Alnus glutinosa was assessed by microscopic analysis of bacterial cells and released fungal conidia, and by the number of operational taxonomic units (OTUs) from denaturing gradient gel electrophoresis using two different primer pairs targeting the rDNA of fungi (ITS2 and 5' end of the 18S region) and bacteria (V3 region and V6-V8 regions). Fingerprints of fungal and bacterial DNA showed a higher diverse microbial community on decomposing leaves than that assessed by microscopy-based techniques. Higher number of OTUs was obtained with primers targeting the ITS2 region of fungi, but the selected primers for bacteria showed similar number of OTUs. A succession of fungal or bacterial taxa throughout leaf decomposition was found, regardless of the chosen primer. These microbial communities ensured a rapid decomposition of submerged leaf litter (k=-0.045 day(-1)). Fungal biomass (up to 58 mg g(-1) AFDM) contributed with more than 98% to the total microbial biomass, supporting a greater role of fungi than bacteria in leaf-litter decomposition in streams.