Bacterial community compositions (BCC) associated with the cladoceran Bosmina coregoni and the cyclopoid copepod Thermocyclops oithonoides in oligotrophic Lake Stechlin versus eutrophic Lake Dagow (northeastern Germany) were compared using molecular techniques. We also transplanted the zooplankton from their native lake to the other lake, and studied changes in their associated BCC as a result of the modified ambient environment. Bacterial community composition associated with B. coregoni was quite conservative between the oligotrophic and eutrophic lakes, and most of the bacteria belonged to Alpha- and Betaproteobacteria. In contrast, BCC associated with T. oithonoides was highly variable and dependent on the environment, and Betaproteobacteria and Bacteroidetes were the most represented among the bacteria. Thermocyclops oithonoides from the oligotrophic lake was more able to retain its bacteria after being transplanted to the eutrophic lake than vice versa. This suggests that bacteria in oligotrophic water were more firmly attached to the copepod and better in resisting environmental fluctuations than those in eutrophic water.