Tetrahymena thermophila, a single-celled ciliate, is a model organism used for studying eukaryote cell processes. The somatic and germline genomes of this organism are separated into two different nuclei. The germline micronucleus (MIC) gives rise to the somatic macronucleus (MAC). Genome rearrangements occur during macronuclear differentiation; similar events have been observed in other ciliates as well as in humans. The MIC of Tetrahymena has been sequenced but not finished; the sequence remains incomplete. We sequenced the MIC region involved in one genome rearrangement, using polymerase chain reaction to amplify micronuclear DNA fragments from this region, then cloning and sequencing them. These new sequences were used to correct and finish this region of the MIC sequence assembly. Further, polymorphisms between the two inbred strains of Tetrahymena used for genetic mapping studies were discovered. The complete and corrected sequence of this region will facilitate an understanding of the mechanism of these genome rearrangement events in eukaryotes.