This 45-day study evaluated the colonization ability of a commercial probiotic mixture (Sanolife PRO-W, containing Bacillus subtilis-complex and Bacillus licheniformis) in the gut of Litopenaeus vannamei reared under Biofloc Technology (BFT) and clear water (CW) systems. The probiotic was added to the culture water every 48 hours at 0.5 mg/L. Intestinal bacterial abundance of Bacillus sp. and Vibrio sp. was quantified using fluorescence in situ hybridization (FISH). Total gut bacterial density was highest in BFT with probiotic (3.67 ± 0.18 × 10^8 cells/g), followed by CW with probiotic (2.12 ± 0.30 × 10^8 cells/g), compared to non-supplemented treatments (~1.53–1.65 × 10^8 cells/g). Bacillus abundance was significantly higher in probiotic-treated groups (0.63–0.69 × 10^8 cells/g), representing 32.85% of total bacteria in CW and 17.26% in BFT. In contrast, Vibrio sp. percentages dropped from ~17.7% in unsupplemented tanks to 1.75% in BFT and 3.54% in CW when probiotics were applied. Water quality parameters were not altered by probiotic addition. Overall, water-administered Bacillus effectively colonized the gut and competitively excluded Vibrio in both culture environments.