The maintenance of genetic integrity during the eukaryotic cell cycle requires sister chromatid cohesion and chromosome condensation. I show that Ycs4p, a subunit of the condensin complex, has an important role in sister chromatid cohesion. My data suggest that Ycs4p functions in a distinct sister chromatid cohesion pathway from that mediated by the cohesin subunit Mcd1p. First, the two proteins localize independently on chromatin. Strikingly, and in contrast to cohesin mutants, a loss of Ycs4p-mediated cohesion can be efficiently re-established within mitosis following reactivation of the protein. Finally, Ycs4p appears specifically required for chromosomal arm cohesion but not at centromeric nor telomeric loci, whereas cohesins are needed throughout the chromosome length. Together these data demonstrate that Ycs4p is involved in a previously uncharacterized cohesin-independent mechanism for chromosome pairing in the budding yeast. This cohesion mechanism provides a unique opportunity to gain mechanistic insight into cohesin function and supports synapsis-based models for cohesin-dependent sister chromatid pairing.