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).

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.

During investigations into freshwater fungi from the Great Mekong Subregion, four Distoseptispora taxa were collected from China and Thailand. Based on morphological characteristics, and phylogenetic analyses of combined LSU, ITS, SSU, TEF1-α, and RPB2 sequence data, two new species Distoseptispora bangkokensis and D. lancangjiangensis are introduced, and two known species D. clematidis and D. thysanolaenae were first reported in freshwater habitat. Illustrations and descriptions of these taxa are provided, along with comparisons with extant taxa in the genus.

Neohelicomyces species are a group of helicosporous hyphomycetes with the potential to produce secondary metabolites. During our investigation of helicosporous fungi, six collections were isolated from both terrestrial and freshwater habitats in Guizhou Province, China. Based on multigene phylogenetic analysis (ITS, LSU, tef1α and rpb2), coupled with morphological data, three new Neohelicomyces species, viz. N. guizhouensis, N. helicosporus and N. hydei were established. A list of accepted Neohelicomyces species with molecular data was provided. The strain of Neohelicomyces pallidus (UAMH 10535) was synonymised under N. denticulatus based on molecular data.

Pleurotheciaceae is a genera-rich and highly diverse family of fungi with a worldwide distribution in aquatic and terrestrial habitats. During the investigation of lignicolous freshwater fungi from karst landscapes in Yunnan Province, China, 15 fresh strains were obtained from submerged decaying wood. Based on the morphology and phylogenetic analysis of a combined LSU, ITS, SSU, and rpb2 sequence dataset, Obliquifusoideum triseptatum, Phaeoisaria obovata, Pleurotheciella brachyspora, Pl. longidenticulata, and Pl. obliqua were introduced as new species, P. synnematica and Rhexoacrodictys melanospora were reported as new habitat records, and P. sedimenticola and Pl. hyalospora were reported as new collections. In addition, based on morphological comparisons and phylogenetic analysis, we accepted Obliquifusoideum into in the family Pleurotheciaceae (Pleurotheciales, Savoryellomycetidae). Freshwater habitats are the primary habitats of Pleurotheciaceae species, and Yunnan Province has the highest concentration and species diversity of Pleurotheciaceae in China.