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Although the <i>Pleosporaceae</i> is one of the species-richest families in the <i>Pleosporales</i>, research into less-explored substrates can contribute to widening the knowledge of its diversity. In our ongoing survey on culturable <i>Ascomycota</i> from freshwater sediments in Spain, several pleosporacean specimens of taxonomic interest were isolated. Phylogenetic analyses based on five gene markers (ITS, LSU, <i>gapdh</i>, <i>rbp</i>2, and <i>tef</i>1) revealed that these fungi represent so far undescribed lineages, which are proposed as two novel genera in the family, i.e., <i>Neostemphylium</i> typified by <i>Neostemphylium polymorphum</i> sp. nov., and <i>Scleromyces</i> to accommodate <i>Scleromyces submersus</i> sp. nov. <i>Neostemphylium</i> is characterized by the production of phaeodictyospores from apically swollen and darkened conidiogenous cells, the presence of a synanamorph that consists of cylindrical and brown phragmoconidia growing terminally or laterally on hyphae, and by the ability to produce secondary conidia by a microconidiation cycle. <i>Scleromyces</i> is placed phylogenetically distant to any genera in the family and only produces sclerotium-like structures in vitro. The geographic distribution and ecology of <i>N. polymorphum</i> and <i>Sc. submersus</i> were inferred from metabarcoding data using the GlobalFungi database. The results suggest that <i>N. polymorphum</i> is a globally distributed fungus represented by environmental sequences originating primarily from soil samples collected in Australia, Europe, and the USA, whereas <i>Sc. submersus</i> is a less common species that has only been found associated with one environmental sequence from an Australian soil sample. The phylogenetic analyses of the environmental ITS1 and ITS2 sequences revealed at least four dark taxa that might be related to <i>Neostemphylium</i> and <i>Scleromyces</i>. The phylogeny presented here allows us to resolve the taxonomy of the genus <i>Asteromyces</i> as a member of the <i>Pleosporaceae</i>.