To gain new insights into the mechanism underlying cytoplasmic male sterility (CMS), we compared the nuclear gene expression profiles of flowers of aBrassica napusCMS line with that of the fertileB. napusmaintainer line usingArabidopsis thalianaflower-specific cDNA microarrays. The CMS line used has aB. napusnuclear genome, but has a rearranged mitochondrial (mt) genome consisting of bothB. napusandA. thalianaDNA. Gene expression profiling revealed that a large number of genes differed in expression between the two lines. For example, nuclear genes coding for proteins that are involved in protein import into organelles, genes expressed in stamens and pollen, as well as genes implicated in either cell-wall remodeling or architecture, were repressed in the CMS line compared withB. napus. These results show that the mt genome of the CMS line strongly influences nuclear gene expression, and thus reveal the importance of retrograde signalling between the mitochondria and the nucleus. Furthermore, flowers of the CMS line are characterized by a replacement of stamens with carpelloid organs, and thus partially resemble theAPETALA3(AP3) andPISTILLATA(PI) mutants. In accordance with this phenotype,AP3expression was downregulated in the stamens, shortly before these organs developed carpelloid characteristics, even though it was initiated correctly. Repression ofPIsucceeded that ofAP3and might be a consequence of a loss of AP3 activity. These results suggest thatAP3expression in stamens depends on proper mt function and a correct nuclear–mt interaction, and that mt alterations cause the male sterility phenotype of the CMS line.