Maintenance of an intact genome and proper regulation of the genes within are crucial aspects for life. The work of this dissertation has implicated the Drosophila condensin II complex in both processes. Condensin II's ability to reconfigure chromosomes into spatially separated and discrete units is necessary to ensure proper meiotic segregation. When this "individualization" activity fails in a condensin II mutant, chromosomes remain entangled, and either cosegregate or become lost during cell division. This leads to the creation of aneuploid sperm. We have also implicated condensin II as a factor necessary to individualize interphase somatic chromosomes from one another. This is relevant in Drosophila because the association of homologous chromosomes is thought to facilitate gene regulation activity in trans. We speculate that condensin II individualization spatially distances aligned chromosomes from one another and prevents this trans-communication between allelic loci. This is supported first by an increase of homologous chromosome pairing in a condensin II mutant background. Secondly, loss of condensin II leads to elevated production from alleles that are known to depend on pairing for transcriptional activation. These meiotic and interphase condensin II roles support its necessity to Drosophila genome integrity and transcriptional regulation. Given the conservation of condensin from bacteria to humans, it is likely that equivalent or related roles exist in a variety of species.