Previous studies on Arabidopsis thaliana and other model plants have indicated that the development of a flower is controlled by a regulatory network composed of genes and the interactions among them. Studies on the evolution of this network will therefore help understand the genetic basis that underlies flower evolution. In this study, by reviewing the most recent published work, we added 31 genes into the previously proposed regulatory network for flower development. Thus, the number of genes reached 60. We then compared the composition, structure, and evolutionary rate of these genes between A. thaliana and one of its allies, A. lyrata. We found that two genes (FLC and MAF2) show 1: 2 and 2: 2 relationships between the two species, suggesting that they have experienced independent, post-speciation duplications. Of the remaining 58 genes, 35 (60.3%) have diverged in exon-intron structure and, consequently, code for proteins with different sequence features and functions. Molecular evolutionary analyses further revealed that, although most floral genes have evolved under strong purifying selection, some have evolved under relaxed or changed constraints, as evidenced by the elevation of nonsynonymous substitution rates and/or the presence of positively selected sites. Taken together, these results suggest that the regulatory network for flower development has evolved rather rapidly, with changes in the composition, structure, and functional constraint of genes, as well as the interactions among them, being the most important contributors.