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Woody substrates were collected in 5 freshwater streams in Hong Kong and the fungi on these substrates were investigated. A total of 153 species were identified, comprising 61 ascomycete and 92 mitosporic taxa, and 20% were previously undescribed. About 30% of the ascomycetes belonged to the genera Annulatascus (Annulatascaceae), Aniptodera, Savoryella (Halosphaeriaceae), Ophioceras, Pseudohalonectria (Magnaporthaceae) and Massarina (Lophiostomataceae). Endophragmiella, Helicosporium and Sporoschisma were common mitosporic genera. Species overlap occurred between different streams, and a few fungi were common in Hong Kong streams. Species composition in the Tung Chung River was distinct, and factors causing variations are discussed. Sampling techniques, the ecological role and distribution of fungi on submerged wood are discussed.