To clarify phylogenetic relationships among Aquanectria, Cosmospora, Fusicolla and other related taxa in Nectriaceae, we examined detailed morphological characters and performed cladistic analyses of a concatenated dataset based on the ITS, LSU and β-tubulin DNA sequences of fungal specimens collected from freshwater habitats in China. A new genus, Cosmosporella, is described to accommodate C. olivacea as its type species. Cosmospora obscura is transferred to Cosmosporella based on morphological similarities and phylogenetic support. Aquanectria jacinthicolor, a freshwater lignicolous taxon, characterized by its orange ascomata and ellipsoid ascospores with broad paraphyses is a newly described freshwater species. This species has affinities with other two known species of Aquanectria and can be distinguished based on ascospore morphology. A specimen with sexual morph of Fusicolla aquaeductuum is reported for the first time.