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Beneficial microorganisms can increase nutrient digestion and absorption in farmed fish. This study investigates the effects of supplemental feeding of Bacillus species isolated from the intestines of wild glass eels on the growth, survival, and gene expression of farm-raised eel larvae for 30 days after hatching. Three species of Bacillus (B. velezensis, AJBV; B. subtilis, AJBS; B. licheniformis, AJBL) without hemolytic activity were isolated, and an experiment compared the growth of eel larvae fed an artificial diet supplemented with each Bacillus species. There were no significant differences in the total length and body depth of eel larvae at 30 days after hatching in all groups. During the feeding period, 149 eels survived from the initial 1000 in the control group. On the other hand, 240, 178, and 141 eels survived in the AJBV, AJBS, and AJBL groups, respectively. However, there were no significant differences in survival rates despite the difference in the number of surviving eel larvae among the groups. In the comparison of gene expression of genes involved with growth (growth hormone, growth hormone receptor 1, insulin-like growth factor II-2) and those involved with digestive enzymes (amylase, trypsin, lipase), there were also no significant differences among the groups. Our results confirm that dietary supplementation with each of the three host-associated Bacillus does not affect the growth and survival rates of eel larvae reared on an artificial diet up to the first 30 days after hatching, nor does it significantly affect related gene expression.