Despite the recognised significance of aquatic hyphomycetes in leaf litter decomposition in streams, few studies have been carried out in the Australian environment and only one prior study in Australian alpine streams (Suter et al. 2011). The Australian alpine environment is distinct from other parts of the world, with a characteristic flora in particular Eucalyptus pauciflora (snow gum), the only native tree species to occur in the alpine area. E. pauciflora have slow breakdown rates, in comparison to other eucalypt species and deciduous Northern hemisphere species. Given the extreme weather fluctuations and the nature of the litter present within the streams, this study investigated the fungal community at both temporal and seasonal timescales in alpine streams of south-eastern Australia. Sporulation, biomass and DNA-based studies combined showed that the fungal community changed over time and seasonally, with the greatest differences occurring between the two extremes of summer and winter. Synchrotron infrared microspectrocopy also revealed internal changes to leaf chemistry as decomposition occurred.