The diversity of freshwater fungi on submerged wood has been documented in three water resources of Mae Chan, Chiang Rai, Thailand. Sixty samples were collected from each site and examined for fungi. In total, 60 fungal taxa were identified including 29 ascomycetes, 27 anamorphic taxa and 4 unidentified species. The data obtained from the three sites were then used to calculate frequency of occurrence, species richness, Margalef index, Simpson's index (D), Shannon-Weiner index (H') and species evenness (E). The fungal diversity from Site 2 (waterfall with abundant trees) was higher than that from Site 1 (river near agricultural zone) and Site 3 (waterfall with scrub). Interestingly, Acrogenospora sphaerocephala, Canalisporium caribense, Corynesporium sp., Didymella aptrootii, Fluminicola bipolaris, Halosarphaeia aquadulcis, Helicomyces roseus and Savoryella lignicola were frequently recorded in all sites. This paper is the first report to provide new data concerning the distribution of freshwater fungi in northern Thailand. The relationship between fungal diversity and freshwater habitats is also discussed.