As a baton in a relay race, intact genomes need to be smoothly passed onto daughter cells every cell generation. Cohesin and condensin are multiprotein complexes involved in chromosome segregation during mitosis, they perform the crucial function of organizing and compacting chromosomes into pairs to facilitate their equal distribution in anaphase. Both complexes share a core of similar origin, containing a heterodimer formed by members of the conserved chromosomal ATPase family named Smc. A third complex containing Smc proteins at its core, the Smc5-Smc6 complex, previously known to be involved in DNA repair has recently been shown to contribute to chromosome segregation during anaphase. Smc5-Smc6 plays a role in the disjunction of repetitive regions. Here, we present results further supporting the importance of Smc5-Smc6 in maintaining the integrity of the repetitive ribosomal DNA (rDNA) locus, the largest repetitive region of the budding yeast genome.