We examined the role of rumen ciliates, using Entodinium caudatum as a model organism, in the detoxification of soluble mercury(II) in vitro under conditions with enhanced or reduced diversity of a co-culture bacterial population as well as the effects of long-term mercury(II) stress on in vitro fermentation parameters and major mercury detoxification products. The E. caudatum growth depended on the capability of the co-culture bacterial population to develop resistance to mercury(II) chloride and on culture conditions. The production of fermentation gas was reduced (P < 0.01) in contrast to methane production. Proportions of volatile fatty acids were affected; however, the total concentration of volatile fatty acids was not influenced. No organic mercury species were detected after long-term application (>1 month) of mercury(II) chloride. The major mercury species was inorganic mercury(II) with substantial accumulation in the bacterial fraction (70%) and less in black sediment (21%) and ciliate fraction (9%) at the 25 micromol/L mercury(II) dose. The data indicate that free-living bacteria protect the ciliate cells by transforming mercury(II) into its insoluble forms.