Genomic libraries of macro- and micro-nuclear DNA of the ciliate protozoan Tetrahymena thermophila were constructed in the bacteriophage vector lambda gt WES lambda B. Screening of these libraries with a probe for the repeated hexamucleotide sequence C4A2 showed many phage from the micronuclear library but few if any macronuclear sequences having homology to this probe. This is consistent with C4A2-repeating elements being present predominantly if not exclusively at or near the termini of macronuclear DNA. Sequences flanking C4A2-repeating elements were isolated from a number of purified phage and were used as hybridization probes to restriction endonuclease digested macro- and micro-nuclear DNA. These experiments revealed a repeated sequence family as well as unique sequences present only in micronuclear DNA. The repeated sequence element appears to be dispersed throughout the genome. Phage-containing individual members of this micronucleus limited sequence family were purified from the micronuclear library. Some of these phage contained sequences which hybidized to macronuclear DNA. These fragments therefore contain a "transition" region between micronucleus-limited sequences and sequences present in both nuclei.