Despite the recognised significance of hyphomycetes in the degradation of leaf litter in streams, few studies have been carried out in alpine environments and none in Australian alpine streams. We hypothesised that the fungal communities responsible for leaf decomposition would change over immersion time, and would respond differently at different sites and on different types of vegetation. Leaf bags containing Epacris glacialis (F. Muell.), Eucalyptus pauciflora (Sieber ex. Spreng) and Eucalyptus delegatensis (R.T. Baker) were deployed at different sites in a stream in the Victorian Alpine National Park, south-eastern Australia. Leaf colonisation was delayed for 2 weeks and decay constants for E. pauciflora and E. delegatensis were 0.004–0.005 and 0.006 respectively. Maximum fungal biomass on leaves was similar to that in previous published studies, whereas sporulation rates were two or three orders of magnitude lower, indicating a reduced reproductive effort. Sporulation and DNA-based studies combined showed that fungal communities on the decomposing leaf material changed over time and exhibited significant preferences for leaf type and study site. We have shown that aquatic hyphomycetes can degrade physically tough leaves of Australian alpine plant species, potentially contributing to pathways for particulate carbon to enter alpine-stream food webs.