The aim of this study was to produce mutant strains of Bacillus subtilis with high probiotic performance for use in the aquaculture of rainbow trout Oncorhynchus mykiss. The main strain of B. subtilis (MS) was irradiated with gamma rays (5.3 KGy). Subsequently, the B. subtilis mutant strain no. 45 (MS. 45) was selected for bacterial growth performance, resistance to acidic conditions, resistance to bile salts and antibacterial activity against Aeromonas hydrophila and Pseudomonas fluorescens. After 60 days, the rainbow trout (70.25 ± 3.89 g) fed with MS. 45 and MS were exposed to hypoxia stress (dissolved oxygen = 2 ppm). Subsequently, immune indices (lysozyme, bacterial activity and complement activity), hematological indices [hematocrit, hemoglobin, WBC, RBC, mean corpuscular volume (MCV)] and antioxidant factors (T-AOC, SOD and MDA)) were analyzed after and before hypoxia exposure. The expression of immunological genes (IFN-γ, TNF-α, IL-1β, IL-8) in the intestine and the expression of hypoxia-related genes (HIF-1α, HIF-2α, FIH1) in the liver were compared between the different groups under hypoxia and normoxia conditions. Growth, immunological and antioxidant indices improved in group MS. 45 compared to the other groups. Stress indices and associated immunologic and hypoxia expressions under hypoxia and normoxia conditions improved in MS. 45 compared to the other groups. This resulted in improved growth, immunity and stress responses in fish fed with the microbial supplement of MS. 45 (P < 0.05) under hypoxia and normoxia conditions, (P < 0.05), resulting in a significant improvement in trout aquaculture.