Randomly collected naturally decaying submerged/semi-submerged wood from six freshwater streams in two forests Doi Inthanon (DI) and Khao Yai National Parks (KY), Thailand was examined for aero-aquatic hyphomycetes following five field collections in July 2009 to November 2010. A total of 1,171 fungal occurrences belonging to 32 species in 13 genera were identified from DI (31%), and KY (28%), with 41 % common to both sites. Of these, eighteen were new records (56.25% of all species) for Thailand. Percentage occurrence of fungi at DI streams 1–3 were 30.77%, 35.99%, and 33.33%, respectively; while at streams 4–6 at KY, percentage occurrence was 31.11, 35.56, and 33.33%, respectively. The most common species at both forests (with >10% frequency of occurrence, FO) were Candelabrum brocchiatum (34.5%), followed by Pseudaegerita corticalis (15.4%), and Cancellidium applanatum (12.5%). These fungi were found at five streams in the two forests while Helicomyces roseus (6.3%), Candelabrum microsporum (4.3%) and Helicosporium panachaeum (4.3%) are regarded as common species. Seven species were regarded as rare, occurring only once per site with FO = 0.1% (Candelabrum sp., Helicoma atroseptatum, H. perelegans, H. resinae, Helicoma sp., Helicosporium aureum and H. gracile). A comparison of the fungal community at the two forests and six streams shows little difference in species composition.