Identification of specific signaling pathways for cardiac hypertrophy in living animals is challenging because no methods have been established to directly observe sequential molecular signaling events at the transcriptional level during pathogenesis. Here, our aim was to develop a useful method for monitoring the specific signaling pathways involved in the development of cardiac hypertrophy in vivo. Expression profiling of the left ventricle by microarray was performed in 2 different mouse models of cardiac hypertrophy: mechanical pressure overload by transverse aortic constriction (TAC) and neurohumoral activation by angiotensin II (Ang II) infusion. To annotate the information on transcription factor-binding sites, we collected promoter sequences and identified significantly frequent transcription factor-binding sites in the promoter regions of coregulated genes from both models (P < 0.05, binomial probability). Finally, we injected a firefly luciferase vector plasmid containing each transcription factor-binding site into the left ventricle in both models. In the TAC and Ang II models, we selected 379 and 12 upregulated genes, respectively. Twenty binding sites for transcription factors, including activator protein 4, were identified in the TAC model, and 4 sites for transcription factors, including ecotropic viral integration 1, were identified in the Ang II model. GATA-binding sites were noted in both models of cardiac hypertrophy. Using the firefly luciferase reporter, we demonstrated the enhancement of transcriptional activity during the progression of cardiac hypertrophy using in vivo imaging in live mice. These results suggested that our approach was useful for the identification of unique transcription factors that characterize different models of cardiac hypertrophy in vivo.