Floral organs are specified by the activities of a small group of transcriptional regulators, the floral organ identity factors. Extensive genetic and molecular analyses have shown that these proteins act as master regulators of flower development, and function not only in organ identity determination but also during organ morphogenesis. Although it is now well established that these transcription factors act in higher order protein complexes in the regulation of transcription, the gene expression programmes controlled by them have remained largely elusive. Only recently, detailed insights into their functions have been obtained through the combination of a wide range of experimental methods, including transcriptomic and proteomic approaches. Here, we review the progress that has been made in the characterization of the floral organ identity factors from the main model plant Arabidopsis thaliana, and we discuss what is known about the processes acting downstream of these regulators. We further outline open questions, which we believe need to be addressed to obtain a more complete view of the molecular processes that govern floral organ development and specification.