Feed additives are essential in improving the growth and immunity of eels, which are often affected by nutritional and disease challenges. This study evaluated the effects of two dietary synbiotics in Japanese eel, Anguilla japonica: Bacillus subtilis with mannooligosaccharide (MOS) and Enterococcus faecium with fructooligosaccharide (FOS). Six diets, including a basal diet (CON), a 4 g kg− 1 oxytetracycline (OTC), and four synbiotic diets - B.subtilis at 1 × 106 and 107 CFU g− 1 plus 5 g kg− 1 MOS (BS6MO and BS7MO) and E. faecium at 1 × 106 and 107 CFU g− 1 plus 5 g kg− 1 FOS (EF6FO and EF7FO) - were prepared and fed to triplicate groups of 20 fish averaging 6.00 ± 0.07g (mean ± SD) for eight weeks. Weight gain (WG) and specific growth rate (SGR), and feed efficiency (FE) of fish fed B. subtilis plus MOS (BSMOS) diets were significantly higher than those of fish fed CON and OTC diets (p < 0.05) but not significantly higher than those of fish fed the E. faecium plus FOS (EFFOS) diets. Best protein efficiency was achieved in fish fed the synbiotics diets (p < 0.05). Fish fed OTC diets showed the highest level of aspartate aminotransferase (AST) but were not significantly different from synbiotic diets, except for BS6MO. Fish fed the EF7FO diets showed the lowest superoxide dismutase (SOD) activity compared to other synbiotics. Japanese eel fed with the synbiotic and OTC diets showed no significant difference in resistance against Vibrio anguillarum. Since synbiotics are dose dependent, the synergetic efficiency of EFFOS is better at 107 CFU g− 1. These results suggest that BS7MO may be more effective as a synbiotic in Japanese eel diet than EFFOS diets. Our results showed that synbiotic diets could improve growth and immunity and be a sustainable alternative to antibiotics.