In many eukaryotic cells, the ribosomal RNA gene (rDNA) is composed of a highly repetitive structure. Previously, we reported the isolation of condensin mutants of Saccharomyces cerevisiae that were defective in carrying long rDNA repeat due to the loss of the replication fork barrier (RFB) protein Fob1p; thus the repeat in the mutants were dramatically contracted. The reintroduction of the FOB1 gene suppressed the contraction of the repeat. It was found that condensin mainly localized at the RFB site in a FOB1-dependent fashion. Here, we show that RNA polymerase I transcription interferes with condensin association with 35S rRNA coding regions in fob1 cells and causes dramatic contraction of rDNA repeat in the fob1 condensin double mutant. Inactivation of RNA polymerase I suppresses the dramatic contraction of the rDNA repeat in the fob1 condensin double mutant. These results suggest that association of condensin with the RFB site outside the active transcription region avoids the dramatic contraction of the rDNA repeat. We also found that the stimulation of RNA polymerase II transcription within the rDNA repeat decreased condensin association with actively transcribed regions. Thus, a characteristic of condensin is that its association with the chromatin is interfered by transcription.