Cecidomyiidae and Sciaridae (Diptera: Sciaroidea) are mostly mycophagous, feeding on decaying plant materials and fungi. On the shiitake bedlogs, great number of larvae of the species cause serious damage, feeding on the mycelium of the shiitake mushroom. We confirmed five species emerged from the shiitake bedlogs, which are two cecidomyiids and three sciarids. Using the DNA barcording, the mitochondrial cytochrome c oxidase subunit I (COI) region (658 bp), the larvae and adult flies were identified, and Camptomyia corticalis was confirmed as a major pest on shiitake mushroom.