Universal minicircle sequence binding proteins (UMSBPs) are CCHC-type zinc-finger proteins that bind the single-stranded G-rich sequence (UMS) conserved at the replication origins of the mitochondrial genome (kinetoplast DNA, kDNA) of trypanosomatids. Trypanosoma brucei expresses two UMSBP proteins, a mitochondrial protein (TbUMSBP1), containing five zinc finger domains, and a nuclear protein (TbUMSBP2), which contains seven such domains. Both the nuclear and the mitochondrial proteins have been previously reported to act in concert in the replication and segregation of kDNA. Yet, only TbUMSBP2 plays a role in nuclear DNA metabolism. Here we report that TbUMSBP2 binds in vitro, specifically and with similar affinities, the kDNA origin-associated sequence UMS and the G-rich strand of the telomeric repeat. TbUMSBP2 colocalizes in vivo with telomeres at the nuclear periphery and is essential for their structure, protection and function. Knockdown of TbUMSBP2 resulted in the clustering of telomeres in one or few foci in the nucleoplasm, phosphorylation of histone H2A at the vicinity of the telomeres, impaired nuclear division, endoreduplication, and cell growth arrest. Moreover, TbUMSBP2 depletion caused rapid reduction in the G-rich telomeric overhang, and an increase in C-rich single-stranded telomeric DNA as well as in extrachromosomal telomeric circles. These observations indicate that TbUMSBP2 is essential for the integrity and function of telomeres. The sequence similarity between the mitochondrial UMS and the telomeric G-overhang and the finding that UMSBPs bind both the mitochondrial and nuclear sequences suggest a common origin and/or function of these interactions in the replication and maintenance of the genomes in the two subcellular organelles. This feature could have converged or preserved during the evolution of the nuclear and mitochondrial genomes from their ancestral (likely circular) genome in early-diverged protists.