How genes change their expression patterns over time is still poorly understood. Here, by conducting expression, functional, bioinformatic and evolutionary analyses, we demonstrate that the differences between the Arabidopsis thaliana APETALA1 (AP1) and CAULIFLOWER (CAL) duplicate genes in the time, space and level of expression were determined by presence or absence of functionally important transcription factor-binding sites (TFBSs) in regulatory regions. In particular, a CArG box, which is the auto-regulatory site of AP1 that can also be bound by the CAL protein, is a key determinant of the expression differences. Because of the CArG box, AP1 is both auto- and cross-regulated (by AP1 and CAL, respectively), and its relatively high-level expression is maintained till to near-mature sepals and petals. The observation that the CArG box was gained recently further suggests that the auto- and cross-regulation of AP1, as well as its function in sepal and petal development, is a derived feature. By comparing the evolutionary histories of this and other TFBSs, we further indicate that the divergence of AP1 and CAL in regulatory regions has been markedly asymmetric and can be divided into several stages. Specifically, shortly after duplication, when AP1 happened to be the paralog that maintained the function of the ancestral gene, CAL experienced certain degrees of degenerate evolution, in which several functionally important TFBSs were lost. Later, when functional divergence allowed survival of both paralogs, CAL remained largely unchanged in expression whereas the functions of AP1 were gradually reinforced by gains of the CArG-box and other TFBSs.