During the course of a project investigating culturable diversity from freshwater sediments in Spain, we isolated 63 strains of cycloheximide-resistant fungi belonging to the order . These well-known ascomycetes, able to infect both humans and animals, are commonly found in terrestrial habitats, colonizing keratin-rich soils or dung. Little is known about their diversity in aquatic environments. Combining morphological features and sequence analyses of the ITS and LSU regions of the nrDNA, we identified 14 species distributed in the genera , , , , , , and . Furthermore, three novel species for the genus are proposed as sp. nov., sp. nov., and sp. nov. The new genera and are introduced based on and , respectively. sp. nov. is characterized and differentiated morphologically from its counterpart by the production of a sexual morph. The novel family is proposed for the genera , , , and , based on their phylogenetic relationships and phenotypic and ecological traits. gen. nov. is introduced to accommodate sp. nov., a fungus with unclear taxonomy related to and . We traced the ecology and global distribution of the novel fungi through ITS environmental sequences deposited in the GlobalFungi database. Studying the fungal diversity from freshwater sediments not only contributes to filling gaps in the relationships and taxonomy of the but also gives us insights into the fungal community that might represent a putative risk to the health of animals and humans inhabiting or transient in aquatic environments.