To investigate the diversity of aquatic fungi, we collected deposits of soil, plants, and plant litter from ponds and streams. NNIBRFG1552 was isolated from soil deposits and NNIBRFG3013 from plant deposits in Namsaengi-mot in Jeju, Korea in 2016; NNIBRFG5472 was isolated from plant litter in Bocheong-cheon, Boeun, Korea in 2018. Based on morphological characteristics and phylogenetic analysis using rDNA sequences of the internal transcribed spacer (ITS), NNIBRFG1552, NNIBRFG3013, and NNIBRFG5472 were identified as Filoporella exilis (100% similarity with KC834046), F. fistucella (99.8% with KC834047), and F. cf. annelidica (100% with KC834044), respectively. Furthermore, cultural and morphological characteristics were analyzed to confirm the molecular identification. No species of the genus Filosporella has yet been reported in Korea.