The hypotrichous ciliated protozoan Oxytricha fallax has both macronuclei and micronuclei. The short DNA molecules of the macronucleus are terminated with repeats of the octanucleotide C4A4. Micronuclear DNA carries a family of long sequence blocks, which share a consensus restriction map and have homology with the C4A4 repeats. Each block contains a 3 to 6 kb subregion, which is refractory to all restriction enzymes tested and includes the C4A4 homology. We conclude that these refractory sequences are at DNA termini because Sau 3A fragments containing them fail to ligate to form circles, and they are rapidly degraded by Bal 31 nuclease. These terminal C4A4-homologous sequence blocks likely represent micronuclear chromosomal telomeres. Possible relationships between these sequences, internal micronuclear C4A4 repeats, and macronuclear DNA termini are discussed.