A comprehensive account of fungal classification from freshwater habitats is outlined and discussed in the present review based on literature of biodiversity studies and recent morpho-phylogenetic analyses. A total of 3,870 freshwater fungal species are listed with additional details on the isolation source, habitat, geographical distribution, and molecular data. The Ascomycota (2,968 species, 1,018 genera) dominated the freshwater fungal taxa wherein Sordariomycetes (823 species, 298 genera) had the largest number, followed by Dothideomycetes (677 species, 229 genera), Eurotiomycetes (276 species, 49 genera), and Leotiomycetes (260 species, 83 genera). Other phyla included in the updated classification of freshwater fungi are: Chytridiomycota (333 species, 97 genera), Rozellomycota (221 species, 105 genera), Basidiomycota (218 species, 100 genera), Blastocladiomycota (47 species, 10 genera), Monoblepharomycota (29 species, 6 genera), Mucoromycota (19 species, 10 genera), Aphelidiomycota (15 species, 3 genera), Entomophthoromycota (6 species, 4 genera), Mortierellomycota (5 species, 3 genera), Olpidiomycota (4 species, 1 genus), Zoopagomycota (3 species, 2 genera), and Sanchytriomycota (2 species, 2 genera). The freshwater fungi belong to 1,361 genera, 386 families and 145 orders. The Pleosporales and Laboulbeniaceae are the largest freshwater fungal order and family comprised of 391 and 185 species, respectively. The most speciose genera are Chitonomyces (87, Laboulbeniomycetes), Verrucaria (50, Eurotiomycetes), Rhizophydium (52, Rhizophydiomycetes), Penicillium (47, Eurotiomycetes), and Candida (42, Saccharomycetes).

Freshwater hyphomycetes are a highly diverse group of fungi with a worldwide distribution and have been mostly reported from tropical and subtropical regions. During investigations of freshwater fungi from the Greater Mekong subregion in China and Thailand, sixteen freshwater hyphomycetes (three of them belong to the class Dothideomycetes while thirteen belong to the class Sordariomycetes) were collected. Based on morphology and multi-gene phylogenetic analyses, Neospadicoides thailandica, Pseudodactylaria aquatica, Sporidesmium nujiangense, Tetraploa thailandica, Vamsapriyaaquatica and Wongia fusiformis are described as new species; Aquapteridospora bambusinum is proposed as a new combination; Acrodictys liputii, Chloridium gonytrichii, Pseudoberkleasmium chiangmaiense, Pleomonodictys capensis, Sporidesmium aturbinatum and Vamsapriya indica are reported as new country records; and Sporidesmium tropicale, Sporoschisma chiangraiense and Sporoschisma longicatenatum are introduced as three new collections. In addition, a checklist of freshwater fungi from China over the last five years is also provided.

Cancellidium is a remarkable fungal genus which has been collected from wood submerged in freshwater and has unique conidia that are important in dispersal in running streams. With such a remarkable morphology, one would have expected it to be a distinct family or order. However, due to the dearth of molecular evidence in related taxa, this genus has previously been placed in the order Hypocreales, subclass Hypocreomycetidae of Sordariomycetes. In this study, we made three new collections of this remarkable aquatic genus from streams in China and Thailand, isolated them into culture, extracted DNA and carried out multigene phylogenetic analysis and divergence time estimation which placed the genus in Diaporthomycetidae. This is one of the seven subclasses of Sordariomycetes and contains 30 lineages that are only known from freshwater. The subclass is therefore of interest when considering the evolution of freshwater fungi. Several lineages of Diaporthomycetidae are morphologically unique and taxa cluster with strong support, but have weak support at the base of the trees. The phylogenetic and MCC trees generated in this study indicate that Aquapteridospora, Barbatosphaeriaceae, Bullimyces, Cancellidium, Ceratolenta, Conlarium, Phialemoniopsis, Pseudostanjehughesia and Rhamphoriaceae are distinct genera/families that evolved in the family/order time frame. The new orders Barbatosphaeriales (177 MYA), Cancellidiales (137 MYA), Ceratolentales (147 MYA), Conlariales (138 MYA) and Rhamphoriales (133 MYA) and six new families, Aquapteridosporaceae (110 MYA), Cancellidiaceae (137 MYA), Ceratolentaceae (81 MYA), Bullimycetaceae (81 MYA), Phialemoniopsaceae (59 MYA), and Pseudostanjehughesiaceae (111 MYA) are introduced with evidence from phylogenies, divergence estimates and distinct morphologies. Of these families, Aquapteridosporaceae, Cancellidiaceae, Bullimycetaceae, and Pseudostanjehughesiaceae are only known from freshwater.

China and Thailand are rich in fungal diversity with abundant freshwater resources that are favorable for numerous fungal encounters. Resulting from this, the majority of the Dictyosporiaceae species reported were from these two countries. During the investigation on the diversity of lignicolous freshwater fungi in the Greater Mekong Subregion, eleven collections of cheirosporous species on submerged wood were collected from lentic and lotic habitats in China and Thailand. Phylogenetic analysis that combined nuclear small-subunit ribosomal RNA (SSU), internal transcribed spacer region (ITS), nuclear large subunit ribosomal RNA (LSU) and translation elongation factor 1α (tef 1-α) loci revealed six new species: Dictyocheirospora chiangmaiensis, D. multiappendiculata, D. suae, Digitodesmium aquaticum, Vikalpa grandispora and V. sphaerica. In addition, four known species were also identified and reported based on morphological and phylogenetic evidence. The detailed descriptions and illustrations of these taxa are provided with an updated phylogenetic tree of Dictyosporiaceae.

The Red River Basin is located in the Indo-Burma biodiversity hotspot and is rich in lignicolous freshwater fungi, but no systematic research has been conducted. A systematic study on the species diversity of lignicolous freshwater fungi in the basin is ongoing. Seven distoseptispora-like specimens were collected from the Red River Basin in Yunnan. Phylogenetic analysis of ITS, LSU, tef1-α, and rpb2 genes and combined morphological data indicate that there are six distinct species of Distoseptispora, including two new species and four known species. Two new species were named D. suae and D. xinpingensis, and the four known species were D. bambusae, D. euseptata, D. obpyriformis and D. pachyconidia. This study provides detailed descriptions and illustrations of these six species and an updated phylogenetic backbone tree of Distoseptispora.

A novel hyphomycetous genus collected from submerged wood in a freshwater stream in Thailand is introduced. The fungus is similar to Tetraplosphaeriaceae species in having subglobose conidial body and elongated setose appendages arising from conidial body. However, its unique combination of macronematous conidiophores and conidia composed with several columns of cells differs it from other genera in Tetraplosphaeriaceae. The phylogenetic analysis based on a combined LSU, ITS and SSU sequence data indicated that our two strains formed a distinct lineage in the family and they cannot be assigned to any existing genera. Therefore, we introduce a new genus Aquatisphaeria to accommodate the new taxa with A. thailandica as the type species. The detailed description, illustration and comparison with related taxa are provided.