Pacific white-leg shrimp (Penaues vannamei), blue shrimp (Litopenaeus stylirostris) and kuruma shrimp (Marsupenaeus japonicus) are the most cultured shrimp species in Europe. In 2020, European shrimp production reached up to 450 tonnes, produced by 25 aquaculture companies using bio-flocs and clear water systems. In addition, 9 companies in Europe serve as hatcheries and produce post-larvae for European shrimp farms. Productions of market-size shrimps as well as post-larvae in Europe are predicted to be increased due to consumer’s preference. No mass mortality of cultured shrimp due to bacterial diseases has been reported from the European shrimp farms. However, effort to minimize bacterial disease outbreaks which may devastate the European shrimp farming is still challenging. Therefore, it is important to understand bacterial community composition in the digestive tract of shrimps including potential pathogens, and compare them to the disease status. Moreover, a robust detection method is needed to predict the pathogenic bacteria rapidly and precisely. We examined bacterial community composition in healthy and diseased shrimp samples covering fresh-water and saline shrimps such as Macrobrachium nipponense, P. vannamei, L. stylirostris and M. japonicus. We found that pathogenic bacteria of the genus Aeromonas, Alteromonas, Flavobacterium, Photobacterium, Pseuodoalteromas, and Vibrio are the most common in the intestines of shrimps. We developed specific primer pairs to detect the thermolabile hemolysin (tlh) gene, a toxin inherent but not exclusively to the Vibrio genera to predict the risk of Vibrio-related disease outbreaks. Here, we developed a SYBR®Green qPCR assay to simultaneously target the tlh gene. Primers were experimentally validated against V. alginolyticus, V. campbellii, V. harveyi, V. parahaemolyticus and V. vulnificus, as well as V. anguillarum and Bacillus subtilis to constrain their taxonomic coverage and determine their specificity for Vibrio, thereby enabling the quantification of pathogenic Vibrio without the need of multiple species-specific markers. We obtained a couple of primers (tlh-G-vibrio-0515-a-S-22: GCTGGTTCTTRGGDCAYTTCTC, tlh-G-vibrio-0771-a-A-22: TGGAACGCYACGGTTRTAGTTC) as the best primer pair candidate that is able to amplify tlh with a melting temperature range of 83.5 - 85°C, a limit of quantification of log 3 gene copies/ng genomic DNA, and a limit of detection at qPCR cycle 34-36. Then, we tested the system over 89 shrimp samples reared in recirculating aquaculture system (RAS) and obtained 21 positive samples with a range of 3.5 ± 1.5 to 4.3 ± 1.6 log copies tlh gene/ng genomic DNA, which equal to 3,200-20,000 Vibrio cells. Our approach offers versatile applications for monitoring and disease prevention management in commercial aquaculture. In addition, this primer pair is also suitable for detecting tlh via conventional PCR.