The macronucleus of the ciliate Tetrahymena contains about 45 copies of the genome. The fraction of the molecules on which an adenine residue is modified to N6-methyladenine is characteristic of the specific site, and consistent between clones. A fragment of DNA containing a site that is uniformly methylated on the macronuclear chromosome was moved to a new location on the extrachromosomal rDNA. The methylation pattern of the fragment on the rDNA was different from that on the chromosome. The data suggest that DNA sequence is not sufficient to determine the level of methylation.