This paper documents a multi-level microcosm system: Dreissena-ciliates-bacteria-viruses. In the first comprehensive investigation of endocytobionts present in the cytoplasm of endosymbiotic ciliates from mussels, bacteria are described from Conchophthirus acuminatus and an undescribed Ophryoglena sp. species which are, respectively, commensal and parasitic in the freshwater bivalve Dreissena polymorpha. Light microscopy, electron microscopy, Feulgen staining, and in situ observation indicated that in some populations of C. acuminatus practically all individuals were infected with cytoplasmic bacteria. Some of these bacteria were in the α-subgroup of proteobacteria. In situ hybridization indicated that some other eubacteria with a very similar morphology were also present in the cytoplasm of C. acuminatus. Using in situ hybridization with appropriate oligonucleotide probes, a large amount of bacteria, most of which were also in the α-subgroup, were observed in the cytoplasm of each specimen of Ophryoglena sp. examined. Some bacteria with virus particles were also observed in a population of the Ophryoglena sp. The bacteria in C. acuminatus were not likely the same as in the Ophryoglena sp. The presence of α-subgroup proteobacteria in the cytoplasm of both endosymbiotic ciliates, in conjunction with previous reports of these bacteria in free-living species, indicates that they are widely established endocytobionts in these protists.