The Thai freshwater fungi are reviewed. Substrates range from baits (Dipterocarpus alatus, Licuala longicalycata and Xylia dolabriformis) to submerged natural wood, collected in northern (Chiang Mai and Chiang Rai), and southern (Narathiwat) and northeastern (Nakorn Ratchassima) parts of the kingdom. The checklist comprises 173 identified species (including 34 Ingoldian fungi) published up to the end of 2010 and is supported with references. The taxa belong to 112 genera, including 30 Sordariomycetes, 12 Dothideomycetes and 70 anamorphic genera. The most frequently collected genera are the hyphomycetes Biflagellospora, Canalisporium, Dactylaria, Dictyosporium and Xylomyces. Five new genera and 26 new species were first described from Thai freshwater habitats. Fungal diversity in different substrates and Sørensen's index in different sites are discussed.