Freshwater ecosystems have a large reserve of latent biological resources that play an essential ecological role, and have significant economic and social value. Fungi in freshwater are prospective materials that can be used in the food, medicine, and biomass energy fields. In this study, three promising fungal species were isolated from freshwater ecosystems in Korea. These isolates were identified as Mortierella biramosa, Paraphoma radicina, and Sordaria macrospora, based on their cultural and morphological characteristics, as well as molecular phylogenetic analyses. These species were previously unknown in Korea. The finding allows us to explore its physiological and biochemical characteristics in more detail and use them as biological resources.