Surfaces of marine invertebrates are colonized by different microorganisms, resulting in formation of diverse microbial communities. Recent studies on jellyfish microbiomes, revealed presence of diverse and specific bacterial communities, which differ between environments, jellyfish populations and are distinct from seawater assemblages. Using molecular biology (denaturing gradient gel electrophoresis (DGGE) and bacterial gene clone libraries) and culture based methods, and different microscopic techniques (epifluorescence and scanning electron microscopy (SEM)), we examined the presence of bacteria on jellyfish, regularly present in the Gulf of Trieste, Aurelia sp., Chrysaora hysoscella and Cotylorhiza tuberculata. Results confirmed that bacterial communities associated with jellyfish are distinct from sea water assemblages. Bacterial community composition differs between different jellyfish species and between individual body parts of medusa. SEM microscopic technique revealed that the jellyfish epidermis contains numerous cnidocytes and is densely covered by cilia. Surface is covered with thin mucus layer, that dissolute off the surface in form of mucus sheets. Using microscopy, presence of bacteria was detected exclusively in mucus. Based on the 16 rRNA gene taxonomic analysis, bacteria of classes Alphaproteobacteria and Gammaproteobacteria, among them Ruegeria, Phaeobacter, Pseudoalteromonas, Vibrio and Alteromonas, and genera Burkholderia, Cupriavidus and Achromobacter of the class Betaproteobacteria, were present in the association. Additionally, results showed that in semi- closed ecosystem, the Big Lake of Mljet Island (South Adriatic), the year-round presence of jellyfish Aurelia sp. 5, may affect the community composition of natural bacterial assemblage. With enrichment experiment we showed, that bacterial degradation of whole dead jellyfish is slower, in comparison with homogenized jellyfish. Degradation resulted in change of bacterial community structure and accumulation of ammonium and orthophosphate.