In river ecosystems, fungi play a critical role in uptaking and transferring allochthonous (terreginic) organic matters into the higher trophic levels. These fungi may also use autochthonous organic matters produced by sessile algae. However, little is known on how supply of autochthonous organic matters affects epilithic fungal assemblages. In this study, therefore, we assessed experimentally effects of these resources on fungal species richness and taxonomic composition by growing them on submerged tiles in transparent and shaded pipes placed at three different sites along the Natori River, Japan. The experiment was done from August to September 2012 and fungal species was examined as OTU. The experiment showed that fungal species richness was significantly higher in light than in dark conditions regardless of sites but effects of light on the species composition differed largely between the sites where was differed in allochthonous inputs. These results indicate that some epilithic fungal species use preferentially autochthonous organic matter and that fungal assemblages change depending not only on authochthonous input but also light conditions.