Abstract:[Objective] Despite the extensive studies about the effects of Bacillus licheniformis on the immune response, disease resistance, and nutrition of Penaeus vannamei, little is known about the effects on the intestinal and environmental microbial communities of P. vannamei in the zero-water exchange aquaculture system. [Methods] The intestinal, seawater, and sediment samples were collected from the environment supplemented with B. licheniformis in food or water for 16S rRNA gene sequencing and linear discriminant analysis effect size (LEfSe). [Results] AddingB. licheniformis had little effect on the growth of P. vannamei, and different adding methods had little effect on the intestinal microflora. However, the addition of B. licheniformis changed the intestinal microbial community and improved the immunity of P. vannamei. [Conclusion] The findings help us to comprehensively understand the changes in shrimp intestine and environment after B. licheniformis is added in feed and water in the zero-water exchange aquaculture system, thereby providing basic information for choosing the right probiotics and addition ways to sustain the health of P. vannamei.