Probiotics, especially Bacillus species, have gained attention for their potential to improve growth and strengthen disease resistance in cultured shrimp. This study evaluated the effects of native Bacillus strains on growth performance, disease resistance and gut microbiota of Penaeus vannamei through the rearing water. The shrimp were reared in water supplemented with different treatments: (a) a negative control (no bacterial addition), (b) a commercial Bacillus spp.® product (positive control), (c) B. subtilis and (d) B. cereus, every 7 days over a period of 21 days. Shrimp reared with B. cereus showed significantly increased specific growth rate (SGR) and average daily gain (ADG) among treatments as compared to the control group (p < 0.05). There was no significant difference in final body weight and feed conversion ratio among groups (p > 0.05). After Vibrio parahaemolyticus challenge, the cumulative mortality was lowest in the B. cereus treated group, showing the highest disease resistance. Alpha diversity of gut microbiota was not significantly different among groups, but beta diversity analyses showed significant differences of gut microbial community structure and LEfSe identified the genus Bacillus as a significant biomarker of the B. cereus-treated group, confirming its colonization in shrimp gut. The results suggest that supplementation of water with a native B. cereus strain enhances growth efficiency and disease resistance and leads to a stable colonization of Bacillus in shrimp gut, offering a practical probiotic approach for intensive shrimp aquaculture.