Salinity of 15‰ increased the nutrient digestion in tilapia initially; however over time this positive effect disappeared. The negative effect of a high dietary soybean meal (SBM) content on intestinal morphology was enhanced at salinity of 15‰. The interaction between salinity and diet composition on intestinal morphology was aggravated with time. SBM-induced enteritis were pronounced in proximal intestine, salinity-induced enteritis were obvious in distal intestine.