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Asexual morphs of freshwater fungi have been mostly reported from tropical and subtropical regions. From our ongoing investigation of the diversity and taxonomy of freshwater microfungi in Thailand, a country with rich natural resources and diverse ecosystems, <i>Parafuscosporella ellipsoconidiogena</i> sp. nov. and <i>P. obovata</i> sp. nov., collected from decaying submerged twigs at Phalad Waterfall in a conserved forest in Chiang Mai Zoo, Chiang Mai Province, northern Thailand, are proposed. DNA phylogenies based on a combination of ITS and LSU datasets support the placement of these species in <i>Parafuscosporella</i> (Fuscosporellaceae, Fuscosporellales, Sordariomycetes), and these two novel species differ from known species in terms of morphology. Detailed descriptions, illustrations and a key to <i>Parafuscosporella</i> species are provided, as well as comparisons with other accepted <i>Parafuscosporella</i> species.