This study investigated the effects of integrating biofloc with microalgae on growth performance and immune gene expression in red tilapia (Oreochromis sp.). The experiment consisted of four treatments: C (Biofloc), T1 (Chlorella vulgaris and Nannochloropsis sp.; 1:1), T2 (Biofloc + Chlorella vulgaris and Nannochloropsis sp.; 1:1), T3 (Biofloc + Chlorella vulgaris and Nannochloropsis sp.; 2:1) in 500 L plastic tanks for 60 days. T2 and T3 exhibited the lowest ammonia and nitrite levels, respectively. T3 exhibited the highest chlorophyll a and chlorophyll b levels, while T2 showed the highest carotenoid content. T2 showed the highest weight gain (142 ± 0.7 g) and SGR (1.61 ± 0.02) and the lowest FCR (1.79 ± 0.009). T2 exhibited the highest gene expression levels in the intestine, with 7.8-fold upregulation of the cathepsin L (ctsl) gene, 3-fold upregulation of toll-like receptor 7 (tlr7), 6.7-fold upregulation of interleukin-1 b (il-1b), 4.7-fold upregulation of tumor necrosis factor-alpha (tnf-a), and 2.8-fold upregulation of metallothionein (mt). In the head kidney, the mt upregulation was highest in T3 (7.2-fold), while tnf-a and tlr7 upregulations were highest in T2 (5.9-fold and 5-fold, respectively). In the liver, the gene expressions were highest in T3, with 6.4-fold upregulation of mt, 5-fold upregulation of ctsl, 2.7-fold upregulation of tlr7, 3-fold upregulation of il-1b, and 5.4-fold upregulation of tnf-a. These results suggest a synergistic effect of algae and bacteria on immune and antioxidative capacity in red tilapia.