Question Large increases in gelatinous zooplankton populations have occurred in many coastal and estuarine ecosystems worldwide because of eutrophication, climate change, and anthropogenic activities which have greatly altered the natural marine environment. Jellyfish release nutrients and dissolved organic matter which may stimulate bacterioplankton growth. However information about the community structure of the bacteria associated with ctenophores is rare. Methods Four ctenophores species Mnemiopsis leidyi, Beroe sp., Bolinopsis infundibulum and Pleurobrachia pileus were sampled at Helgoland Roads in the Germany Bight, North Sea from Oct.2009 to Oct. 2010. Each individual was washed 5 times with sterile seawater to remove transient and loosely associated microorganisms from the surfaces of ctenophores, and then total genomic DNA was extracted from freeze-dried tissue. Automated Ribosomal Intergenic Spacer Analysis (ARISA) fingerprinting and 16S ribosomal amplicon pyrosequencing were performed to investigate the structure and diversity of the bacterial communities associated with ctenophores. Results We revealed significant differences between associated-bacterial communities among different ctenophores species based on ARISA fingerprinting (P<0.001). Based on 16S ribosomal amplicon pyrosequencing, Proteobacteria (87%-98%) were the majority of the predominant bacteria in ctenophores. Within the Proteobacteria, M. leidyi and P. pileus mainly harbored Gammaproteobacteria, Marinomonas made up the majority of the predominant Gammaproteobacteria in M. leidyi. Conversely, in P. pileus the Gammaproteobacteria were mainly composed of the genera Pseudoalteromonas and Psychrobacter. The bacterial community of B. infundibulum comprised of 46.5% Alphaproteobacteria and 52.71% Gammaproteobacteria which in specific were Thalassospira and Marinomonas. Beroe sp. was mainly dominated by Alphaproteobacteria, particularly by the genus Thalassospira. Conclusion 1. Bacterial communities associated with ctenophores displayed a low diverse and highly species-specific character. The genus Marinomonas, Pseudoalteromonas, Psychrobacter and Thalassospira are the predominant groups. 2. Bacterial communities associated with ctenophores were consistently divergent from those presented in the surrounding sea water which has been reported before.