The aim of this study was to evaluate the Zn sensitivity of Euplotes vannus, Euplotes crassus, and their naturally associated bacteria sampled from sediments in the northwest and east regions of Guanabara Bay. The unexposed ciliates and bacteria did not appear to be negatively affected by 96 h of assay. In the control group, E. vannus exhibited an increase in the biomass content from 2.3 × 10(2) to 2.3 × 10(3) μg C cm(-3) between 0 and 96 h, and E. crassus increased up to 7.07 × 10(2) μg C cm(-3) at 48 h. The maximum biomass was pointed by E. crassus (1.33 × 10(3) μg C cm(-3)) in the presence of 0.005 mg Zn L(-1) and E. vannus was naturally associated bacteria (2.40 × 10(-1) μg C cm(-3)) in the presence of 1.0 mg Zn L(-1) (96 h). The growth of E. vannus from the northwest region showed concentration-dependent manners, and it is more sensitive to zinc than E. crassus from the southeast. Naturally associated bacteria showed better adaptation to increasing concentrations of Zn, and the Dunnett test showed that previous environmental selection is important. These results show that new bioremediation tools are necessary.