The infection characteristics with scuticociliates at on-land rearing farms and hatcheries of flounder, Paralithys olivaceus was investigated during the year of 2001 by juvenile infection routes. When culture tanks for living food organisms such as chlorella, rotifer, and Artemia were searched, scuticocilates were detected both in live and dead rotifer, and at the dregs of culture tank bottoms at almost hatcheries. When rotifer infected with scuticocilates fed on fish larvae, lots of scuticocilate were inhabited at the bottom of fry rearing tanks. After feeding on scuticocilates-infected rotifer on fish larvae, first infection was detected at 10 days after bottom dwelling or 40 days old after hatching. By histopathological examination we confirmed the infection route of eyeball or brain contamination was that the ciliate worms digged through mouth and front part of the dosal fin cuticle, transferred into eyeball along the epithelium and muscle tissue, and reached finally into brain by the muscle and nerve tissue. The infection of internal organs was clarified into two routes. The first route was started from the infection at ventral and anal fin rays by the worms, and reached at the anus and rectum through the epithelium and muscle tissue. The second route was initiated from the infection at urinary organ and reached into the rectum epithelium cells, inner wall of intestine, abdominal cavity, pancreas, kidney, and pancreas. At seed production farms where fish larvae fed on scuticocilate-free rotifer, the worms were not detected not only at the food organisms culture tanks and juvenile rearing tanks but also larval flounder less than 7cm in total length.