Fluorescence imaging using synthetic probes is becoming increasingly popular as a chemistry-based technique for the analysis of biomolecules. Real-time visual information on various biological molecules can be obtained by designing probes with high flexibility. The focus of our research is to design fluorogenic probes which are non-fluorescent in their initial intact form, but exhibit enhanced fluorescence intensity upon reactions with target biomolecules. The fluorescence switch of these probes allows the detection of the function and the localization of biomolecules with a high signal-to-noise ratio. Thus far, we have succeeded in designing and synthesizing fluorogenic probes that visualize molecules involved in epigenetics. Histone deacetylases (HDACs) play an important role in the epigenetic regulation of gene expression. A significant amount of epigenetic information can be obtained by the detection of enzyme activity. However, the existing methods require complicated multistep procedures. To overcome this limitation, we developed fluorogenic probes for the detection of HDAC activity in a one-step procedure. In this review, the details of the strategy for probe design and the detection method have been described.