During investigations of freshwater ascomycetes we found one interesting taxon from Aomori (Japan), as well as three additional taxa from North Carolina (USA), which were morphologically similar to Minutisphaera, a recently described freshwater fungus in the Dothideomycetes. The ascomata of all the collections bore dark hair-like structures around the ostiolar region, obovoid to obclavate bitunicate asci, and one to three septate hyaline to brown ascospores with a sheath (in material from Japan), and with both sheath and appendages (in material from the USA). The apothecial ascomata of these taxa, however, differ from those of the type species of the genus, which are perithecial. Two collections of Minutisphaera-like fungi from the USA were morphologically quite similar but differed in ascospore size. To assess the phylogenetic affinities of Minutisphaera-like taxa with the type species, M. fimbriatispora, we sequenced 18S and 28S nrDNA of five newly collected strains of Minutisphaera. We also sequenced the nrDNA for the entire internal transcribed spacer region of 10 strains to assess interspecific and intraspecific variation with M. fimbriatispora. Additionally we examined the secondary metabolite profiles of two strains from USA. Based on maximum likelihood and Bayesian analyses of combined 18S and 28S, and separate ITS sequences, as well as examination of morphology, we describe and illustrate a new species, M. japonica. One collection from North Carolina is confirmed as M. fimbriatispora, while two other collections are Minutisphaera-like fungi that had a number of similar diagnostic morphological characters but differed only slightly in ascospore sizes. The phylogeny inferred from the internal transcribed spacer region suggested that two out of the three North Carolina collections may be novel and perhaps cryptic species within Minutisphaera. Organic extracts of Minutisphaera from USA, M. fimbriatispora (G155-1) and Minutisphaera-like taxon (G156-1), revealed the presence of palmitic acid and (E)-hexadec-9-en-1-ol as major chemical constituents. We discuss the placement of the Minutisphaera clade within the Dothideomycetes. The description of the genus Minutisphaera is emended to accommodate M. japonica within Minutisphaera. Abstract: During investigations of freshwater ascomycetes we found one interesting taxon from Aomori (Japan), as well as three additional taxa from North Carolina (USA), which were morphologically similar to Minutisphaera, a recently described freshwater fungus in the Dothideomycetes. The ascomata of all the collections bore dark hair-like structures around the ostiolar region, obovoid to obclavate bitunicate asci, and one to three septate hyaline to brown ascospores with a sheath (in material from Japan), and with both sheath and appendages (in material from the USA). The apothecial ascomata of these taxa, however, differ from those of the type species of the genus, which are perithecial. Two collections of Minutisphaera-like fungi from the USA were morphologically quite similar but d...