In order to study the flora structure in the intestinal tract and the virus-carrying condition of the different aquatic farm shrimps, we used conventional method of bacteria isolation, cultivation, purification and bacteria 16SrDNA sequences analysis to analyze the total number of culturable bacteria, the species and numbers of dominant bacteria and we used Nested polymerase chain reaction (Nested PCR) method to detect shrimp virus in Litopenaeus vannamei and Fenneorpenaeus chinensis cultivated in different farms of Jiangsu, Shandong and the Republic of Korea. The results showed that the total number of culturable bacteria of Litopenaeus vannamei and Fenneorpenaeus chinensis is between 10⁵ and 10⁹ CFU/g, and identified the dominant bacteria isolated from the intestinal tract to genus (species). The results showed that the dominant bacterial respectively belong to Lactococcus sp, Vibrio sp, Bacillus sp, Photobacterium sp, Shewanella sp, Arthrobacter sp and Microbacterium sp. Litopenaeus vannamei and Fenneorpenaeus chinensis samples are tested positive for WSSV, 6 batches of shrimp samples which were tested positive WSSV, are isolated Vibrio sp from intestinal tract, accounting for 33%-93.58% of culturable bacteria, 2 batches of shrimp samples which were tested positive WSSV, are isolated Shewanella sp, from intestinal tract, accounting for 21.67%-34.21% of culturable bacteria, 4 batches of shrimp samples which were tested positive WSSV, are isolated Photobacterium sp, from intestinal tract, accounting for 21.03%-66.83% of culturable bacteria.