Abstract: A feeding trim was conducted to investigate the effects of soybean oligosaccharides (SBOS) on the digestive en-zymes activity, feed digestibility and intestinal morphology in juvenile Japanese flounder (Paralichthys olivaceus). Four isonitrogenous and isocaloric practical diets (crude protein 49%, gross energy 19 kJ/g) including only fish meal (FM) or soy protein isolate (SPI) as a sole protein source with (Diets FMO and SPIO) or without (Diets FM and SPI) supplemen-ted SBOS (stachyose, 2.61%; raffinose, 0.61%) were formulated. Each diet was randomly assigned to triplicate aquaria stocked with 30 fish (initial body weight 1.93±0.02 g) each. Fish were maintained in flow-through aquaria at water temperature ranging from 22.0℃ to 25.0℃ and fed twice (08:00 and 16:00) daily to apparent satiation for 8 weeks. Pepsin/protease activities in alimentary tract and liver were generally decreased by supplemental SBOS, but the difference was not significant (p0.05). Supplementation with SBOS significantly decreased the amylase activity in midgut, in-creased in stomach (p0.05). Supplemental SBOS significantly increased the amylase activity in stomach and foregut, decreased in midgut (p0.05). At the same time, dietary SBOS supplementation significantly decreased the apparent digestibility coefficients (ADC) of dry matter, increased the crude lipid and energy (p0.05). ADCs of dry matter, crude protein, crude lipid and energy of Diet SPI were not significantly affected by dietary supplemental SBOS (p>0.05). Intestinal morphology was not obviously influenced by dietary supplemental SBOS in fish fed FM or SPI-based diets. These results indicated that dietary supplemental SBOS did not negatively affect the digestion of Japanese flounder and SBOS was not the main factor which affected the utilization of soy protein sources.