The mycobiota on dead submerged plant parts of Phragmites australis reed (leaves, stems, leaf sheaths) was studied in lakes – Pleshcheyevo, Mostetskoye, a lake in the Zavolzhsky district of Yaroslavl and the Kotorosl river (Yaroslavl region, Russia). The kingdom Fungi is represented by 53 species belonging to 33 genera, 25 families, 12 orders, and 7 classes in 2 taxonomic phyla: Mucoromycota (4 species), Ascomycota (48). The kingdom Chromista (fungi-like organisms) includes 8 species belonging to 3 genera, 2 families, 2 orders, and 1 class under phylum Oomycota. For the first time, 23 species of micromycetes were found on reeds. Representatives of the orders Pleosporales (16 species), Helotiales (11), Saprolegniales (7), Hypocreales (5) prevailed. The number of species of fungi on fragments of plants in different aquatic bodies varied from 16 to 39, the statistically significant difference in the species composition of communities of dead reeds was found between a lake in the Zavolzhsky district of Yaroslavl and the Kotorosl River (R = 0.646, significance level of sample statistic 0.1%).