Cobia (Rachycentron canadum) is a marine finfish with good potential for mariculture. This study analyzes the effects of probiotic Bacillus spp. on the performance of cobia larvae reared in a recirculating aquaculture system (RAS). Larvae were stocked into two independent RAS for 26 days after hatching. One of the systems (Probiotic treatment) received the addition of a commercial probiotic consisting of B. subtilis, B. licheniformis and B. pumilus directly into the water and by live feed. Survival, final weight and water quality were not affected by probiotics. Results showed larvae of the probiotic treatment demonstrated a greater resistance to salinity stress. Immunohistochemical analysis showed a higher expression of CD4 in probiotic treatment. These results suggest that Bacillus spp. probiotics used in RAS have a potential stimulating impact on immune system differentiation and increases salinity stress resistance of cobia larvae.