Different modes of asexual and sexual reproduction are typical for the life-history of metagenetic Scyphozoa. Numerous studies have focused upon the general life history distribution, reproductive behavior, factors leading to strobilation, growth rates and impact of predation rate of medusa. However, bacteria associated with different life stages of Scyphozoa have received less attention. In the present study, bacterial communities associated with different body fractions and different life stages of two Scyphomedusae Cyanea lamarckii and Chrysaora hysoscella, which are common species in the German Bight, North Sea, were analyzed via automated ribosomal intergenic spacer analysis (ARISA). Regarding to the analysis of different body fractions (umbrella, gonad, tentacle and mouth arm), significant differences are revealed between umbrella and other body fractions (gonad and tentacle) in terms of the associated bacterial community in both species. With regard to the different life stages, bacterial community structure varied from the early stage planula larvae to polyp even to adult medusa with significant differences in both species by multivariate analysis. Furthermore, the free-living and attached bacterial community of food source did not influence the bacterial communities of polyps, however, polyps displayed a significantly different bacterial community in response to different food source. The bacterial community associated with scyphozoan presented species-specific structure.