In order to improve the present running seawater system for seedling production of marine fishes, rearing experiments with the juveniles of black seabream (Acanthopagrus schlegeli) and oblong rockfish (Sebastes oblongus) were conducted. The recirculating seawater system (F) equipped with the rotating biological contactors and the running seawater system (R) were used. Environmental factors, growth, survival rate and rearing density of the fish were compared between two systems during the experimental period. In the rearing experiment of black seabream, water temperature in F was fluctuated with surrounding air temperature and was higher than that in R. Specific gravity of the rearing seawater in F was relatively stable in the range of 1.0252 to 1.0266, while that in R was greatly fluctuated. pH in F turned out to be 7.51, but pH in R was similar to that in the natural seawater. Dissolved nitrite and nitrate in F were higher than those in R. While no significant differences in the growth of black seabream juveniles were recognized between two systems, survival rates of fishes in F were higher than those of fishes in R. In the rearing experiment of oblong rockfish, water temperature in F was higher than that in R. Specific gravity in F was slightly higher than that in R which showed relatively less fluctuation in the range of 1.0253 to 1.0270. pH in F turned out to be 7.96, but pH in R was similar to that in the natural seawater. Dissolved nitrite and nitrate in F were higher than those in R, but ammonia was lower in F. The juveniles of oblong rockfish reared in F grew significantly faster in their total length and body weight than those in R (P<0.05). However, survival rates of fishes between two systems showed no significant differences.