In Lake Biwa, parasitic fungi infecting phytoplankton may play important roles in seasonal succession of plankton and material cycling. Yet, their diversity was still unknown. Here in this study, fungal community structures were analyzed by next generation sequencing (NGS) based on ITS rDNA. Parasitic fungi attached to large phytoplankton were identified by single-spore analysis based on the 18S and ITS rDNA sequences. NGS showed that 13.5% of fungi was affiliated to Chytridiomycota including 22 species, and 45.8% was Ascomycota, 36.1% was Basidiomycota, and 4.5% was Zygomycota. We found parasitic fungi on various phytoplankton species, such as Asterionella formosa, Aulacoseira granulate, Fragilaria crotonensis and Staurastrum dorsidentiferum. Five species of Chytridiomycota were detected, which are affiliated to Zygorhizidium and Chytridiomyces. More analysis will be done to clarify the roles of diverse fungi in Lake Biwa.