How different organs are formed from small sets of undifferentiated precursor cells is a key question in developmental biology. To understand the molecular mechanisms underlying organ specification in plants, we studied the function of the homeotic selector genes APETALA3 (AP3) and PISTILLATA (PI), which control the formation of petals and stamens during Arabidopsis flower development. To this end, we characterized the activities of the transcription factors that AP3 and PI encode throughout flower development by using perturbation assays as well as transcript profiling and genomewide localization studies, in combination with a floral induction system that allows a stage-specific analysis of flower development by genomic technologies. We discovered considerable spatial and temporal differences in the requirement for AP3/PI activity during flower formation and show that they control different sets of genes at distinct phases of flower development. The genomewide identification of target genes revealed that AP3/PI act as bifunctional transcription factors: they activate genes involved in the control of numerous developmental processes required for organogenesis and repress key regulators of carpel formation. Our results imply considerable changes in the composition and topology of the gene network controlled by AP3/PI during the course of flower development. We discuss our results in light of a model for the mechanism underlying sex-determination in seed plants, in which AP3/PI orthologues might act as a switch between the activation of male and the repression of female development.F lowers are typically composed of four organ types, which are disposed in four floral whorls. From the outside of the flower to the center, they are sepals, petals, stamens, and carpels (the subunits of the gynoecium). The developmental fate of these different types of organs is specified by a small number of floral organ identity genes. The pivotal role of these genes was uncovered through the analysis of mutants that form flowers with homeotic transformations, i.e., the replacement of one type of organ with another (1-4). Based on the morphological defects of the individual mutants and their genetic interactions, it was proposed that the floral organ identity genes act in a combinatorial manner and have distinct functions during flower development, with the so-called A function genes being required for the formation of sepals and petals, B function genes for petal and stamen development, and C function genes for the formation of stamens and carpels. This well-established ABC model of floral organ identity specification (5) has provided, since its introduction more than 20 y ago, an invaluable framework for the analysis of the genetic mechanisms underlying the formation and evolution of flowers.Molecular characterization of the floral organ identity genes in different species revealed that they encode transcription factors and belong, with few exceptions, to the family of MADS domain proteins (1-3). The floral organ identity factors w...