Pathological findings associated with scuticociliatosis in farmed Japanese flounder in Japan are described. Ten moribund fishes, farmed in Tottori Prefectural Fisheries Experimental Station, showed cutaneous ulcers, darkened skin, fin and tail rot, exophthalmia and alterations in swimming behaviour. Histopathologically, severe epidermal degeneration and necrosis, hyperplasia of branchial epithelium, myositis, myelitis, encephalitis associated with heavy accumulation of scuticociliates in the periorbital cavity and optic nerve fiber were observed. Moreover, masses of ciliates were found to feed on the host tissues such as skeletal muscles, gills and brain, causing severe degenerative changes associated with abundant neutrophilic and lymphocytic infiltration. These findings suggest that the present scuticociliate, Miamiensis avidus, is a highly invasive and destructive pathogen infecting Japanese flounder and capable of developing systemic fatal infection.