Mutation is the ultimate source of all genetic variation and is, therefore, central to evolutionary change. Previous work on the ciliate Paramecium tetraurelia concluded that the presence of a transcriptionally silent germline genome has caused the evolution of a low base-substitution mutation rate in the germline genome of that ciliate. Here, we use mutation accumulation (MA) lines of the ciliate Tetrahymena thermophila to test the generality of this result. We find that both ciliates have similar base-substitution mutation rates in their germline genomes. The estimated base-substitution mutation rate cannot account for the observed fitness decline of the MA lines of T. thermophila, suggesting that it may have been caused other types of mutations.