The marine environment hosts an important bacterial diversity in planktonic form in the water column or in biofilms on biotic and abiotic surfaces. Even if the bacteria in association with animals can be simple epibionts that are not harmful for the animal or human health, pathogenic bacteria can also be identified. For example, the genus Vibrio, naturally occurring in the marine environment, can be isolated from phytoplankton zooplankton bivalve mollusks, fish and shrimps demonstrating the presence of microorganisms at all trophic levels with potential transfers between marine species. In addition, some bacteria in the marine environment may carry antimicrobial resistance genes, posing an additional risk to human health. These resistance genes and more generally the microbial community occurring in the marine environment are still insufficiently identified. With recent advances in molecular biology, culture-dependent methods are gradually replaced by DNA-based techniques (PCR, qPCR) which are known to be faster, more robust and specific for bacterial identification. The 16S rRNA gene sequencing is one of the most used methods for bacterial quantification and identification, due to its presence in almost all bacteria and allowing identification up to the bacterial species. However, there are two major disadvantages to using this genetic marker for these analyses in complex samples. First, the 16S rRNA gene is multicopy, which poses a problem for the quantification of bacterial biomass, leading to its overestimation.