Riboswitches are structured RNA domains usually residing in the 5′-untranslated region of messenger RNAs as RNA sensor elements, which can bind specifically and directly to certain metabolites to induce corresponding changes in their conformation and activate or inhibit the transcription, translation, and splicing of mRNA to regulate gene expression without the need for any regulatory factors. Some riboswitches can be used as novel targets for antibacterial drug discovery. This article reviews the structure of the Flavin mononucleotide (FMN) riboswitch, the mechanism of regulation of gene expression and thermodynamic, kinetic studies for the FMN riboswitch. The design and screen for the new generation of antibiotics based on FMN riboswitch are also discussed.