This is the first genetic analysis comparing cultured endobacteria discovered in the tentacles of cnidarian species (Tubularia indivisa, Tubularia larynx, Corymorpha nutans, Sagartia elegans) with those found in the cerata tips of selected nudibranch species (Berghia caerulescens, Coryphella lineata, Coryphella gracilis, Janolus cristatus, Polycera faeroensis, Polycera quadrilineata, Doto coronata, Dendronotus frondosus). Shared pathogenic activities were found among other microorganisms in the Pseudoalteromonas tetraodonis group (TTX), and the Vibrio splendidus group (haemolytic, septicaemic, necrotic activity). Specific autochthonous endobacteria of extremely low similarity to their next neighbours were detected in nudibranch cerata. These organisms are regarded as new and unknown endobacteria; among them were Pseudoalteromonas luteoviolacea (95%), Orientia tsutsugamushi (84%), Gracilimonas tropica (96%), Balneola alkaliphia (95%), Loktanella rosea (97%). SEM micrographs provide insight into endobacterial aggregates in cnidarian tentacles and nudibranch cerata. Since certain nudibranch predators prey on cnidarian species, it is assumed that cnidarian tentacle bacteria are directly transferred to nudibranch cerata. The pathogenic endobacteria may contribute to the chemical defence of both the nudibranch and cnidarian species investigated.