Thailand is a leading exporter of the black tiger shrimp in the world. Although the global demand is increasing annually, the black tiger shrimp production in Thailand has been falling due to complications in domestication such as poor reproductive maturation and disease outbreak. Despite a better market price of the black tiger shrimp, many farmers have changed to cultivate the Pacific white shrimp, which have far less farming difficulties. To revive the black tiger shrimp production, this project aimed to examine microbial structures between the two shrimp under different growth stages and to determine approaches to enhance disease resistance in the black tiger shrimp. Here, we compared the bacteria profiles in intestines of the black tiger shrimp and the Pacific white shrimp from different growth stages. The bacterial profile analysis by denaturing gradient gel electrophoresis revealed that dominant bacteria in both shrimp species were highly similar. However, the DGGE profile of 20-day-old postlarvae was distinct from those of juvenile stages in both shrimp species. This observation suggested that growth stages had more influences on bacterial population in intestines than shrimp species, when both shrimp species were reared under the same diet and environmental conditions. We further compared intestinal bacterial profiles of the black tiger shrimp and the Pacific white shrimp under no pathogen challenge control and under pathogenic Vibrio harveyi challenge. The DGGE profiles showed that the presence of V. harveyi altered the intestinal bacterial patterns in comparison to the control. This implies that bacterial balance in shrimp intestines was disrupted in the presence of V. harveyi. Furthermore, bacteria were isolated from shrimp intestines and screened for antagonistic activity against V. harveyi. The bacteria isolates will be further tested for feasibility application in shrimp farming to protect against colonization of harmful bacteria in a subsequent project. Besides beneficial bacteria approach, we also investigated on effects of bacterial lipopolysaccharide (LPS) as feed supplement to improve the immunity of the black tiger shrimp. The up-regulation of the immune gene levels in intestines and higher level of resistance to V. harveyi of the shrimp fed with LPS provide the evidence for potential application of LPS as an immunostimulant in shrimp farming. The findings of this work will ultimately lead to alternative disease prevention approaches such as beneficial bacteria as biocontrol agents and immunostimulants to modulate host immune system to increase shrimp survival.