The high-throughput Miseq sequencing technology was used to analyze the microbiota structure in Litopenaeus vannamei larvae, intestine and gill of young Litopenaeus vannamei under the condition of seawater and fresh water. The sequence results revealed that Firmicutes and Proteobacteria dominated in the larvae, intestines and gill with great variation in abundance. In particular, Lactococcus accounted for 36.1% in larvae microbiota community, Gammaproteobacteria_ unclassified 25.5%, Bacillus 13.5%, Solibacillus 7.9%, Pseudomonas 5.0% and Arthrobacter 2.5%. In microbiota in gill tissue in both seawater and freshwater, Lactococcus, Bacillus, Solibacillus, Pseudomonas and Arthrobacter were dominant. Regarding to microbiota in intestine from seawater, Photobacterium accounted for 22.9%, Vibrio 18.2%, Lactococcus 13.3%, Cellvibrio 8.0%, Shewanella 5.5%, and Bacillus 5.4%, while in intestine from freshwater Shewanella 57.4%, Lactococcus 18.8%, Bacillus 6.3%, and Vibrio less than 0.1%. These results indicated that culture conditions had less influence on the microflora structure in gill than that while had great influence in intestine.