Fungal infection of the filamentous cyanobacterium Anabaena smithii was observed in Lake Shumarinai in 2004-2006. Two fungal species were found to parasitize the specialized cells of A. smithii. These fungi might not correspond to the chytrid species that the previous studies reported as the parasites for Anabaena species. One fungus showed selective attachment to the akinete (akinete type). The filaments parasitized by this fungus increased in August 2004 and October 2006, when akinete and filament densities also increased. The maximum percentage of parasitized filaments was 3.2% of all filaments in October 2006. The other fungus was usually attached to the heterocyst (heterocyst type). The filaments parasitized by this fungus increased in October from 2004 to 2006. The maximum percentage of parasitized filaments was 20.6% in October 2004. The biomass of A. smithii was not suppressed by akinete-type fungus because of the low percentage of parasitized filaments. The heterocyst-type fungus might disturb the nitrogen fixation, but its effect was negligible due to a high concentration of available nitrogen for planktonic algae in Lake Shumarinai.