Molecular beacon (MBs) are short, single-stranded, hairpin-shaped, and fluorophore-/ quencher-labeled oligonucleotide. They are intensively used for fluorescence turn on detection of target DNA in biological fluids and real-time polymerase chain reaction based on Watson-Crick base pairing. Recently, researchers have also devoted to developing non-Watson-Crick base pairing-based MBs for sensitive and selective detection of heavy metal ions, thiol molecules, enzyme-substrate reaction, sulfated polysaccharides, and cyclic diadenosine monophosphate. In this review article, non-Watson-Crick base pairing-based MBs are introduced and discussed their sensing mechanism in detail.