Woody substrates were collected from the Koito River in Japan, and the biodiversity of fungi on these substrates was investigated. Twenty-eight species were identified, comprising 12 ascomycete and 16 anamorphic taxa. The common fungi included Chaetosphaeria sp., Ophioceras commune, Pseudohalonectria lignicola, and Savoryella lignicola. The occurrence of fungi on submerged wood is discussed, and three interesting taxa – Pseudohalonectria lignicola, Bactrodesmium arnaudii, and B. pallidum – are described and illustrated.