The host-parasite relationships between phytoplankton and fungi are believed to be highly host specific. However, due to difficulties in morphological identification of fungi, their diversity and host specificity is still unknown, especially in the field. In this study, we examined the diversity and host specificity of fungi attached to phytoplankton in Lake Inba. A genomic single-spore method reveals that fungi attached to two dominant diatoms, Aulacoseira granulata and A. ambigua, were affiliated not only to Chytridiomycota (chytrids) but also to Cryptomycota. They are quite diverse at order levels including novel lineages clades. The extent of host specificity differed among species, that some fungi could infect various hosts. This pattern was also confirmed by cross infection experiments with using 5 chytrids and 4 potential host diatoms. 2 chytrids could infect all 4 diatoms, while other 3 chytrids can infect only their own host diatoms. This is the first study to show that parasitic fungi are very diverse, and host specificity varies between fungal species in the field. Single-spore PCR, together with infection experiments, is a useful approach for examining ecological relationships between host and parasites in ecosystems.