The effect of live yeast Rhodoturula glutinis was evaluated on juvenile Oreochromis niloticus cultivated in a Biofloc system. Growth performance and the expression of innate response and relevant oxidative stress genes were evaluated after a 12-week feeding trial. Three experimental treatments were evaluated in a conventional tilapia culture (control), Biofloc culture (BFT), and Biofloc with the addition of the live yeast R. glutinis 1×106 CFU g-1 (BFT+Rg), with four replicates per treatment. In all cases, commercial food was supplied to the organisms (32% protein and 5% lipids). O. niloticus juveniles (7.02 ± 0.04 g) were randomly distributed in 12 tanks, each with 15 animals. BFT+Rg treatment showed a significant increase in weight gain compared with the other treatments. Significant improvements were found in Fulton's condition factor, feed conversion rate, and hepatosomatic index under Biofloc conditions, BFT, and BFT+Rg treatments. No significant differences were observed in survival. R. glutinis directly influenced gene expression in the liver and intestine. The expression of tnfa, tgfb, hsp70, and gpx, genes in the liver significantly increased in the BFT+Rg treatment compared with the other treatments. Similarly, a significant increase was found in intestinal il1b, tnfa, tgfb, trf, hsp70 gpx, and cat expression patterns in the BFT+Rg treatment. Based on the performance and immune response, the present study suggests the use of R. glutinis as a strategy to increase the productivity of tilapia in Biofloc culture.