Photochromic materials have been widely used in many fields such as electro-optical functional materials and novel bio-materials. In this study, six cyanine-based dithienylethene compounds were successfully developed, and their photoisomerization and emission change properties were fully investigated. The results indicated that the UV/vis absorption of pyridinium-based compounds displayed near-infrared absorption, while their fluorescence showed quenching emission as a result of the changes in structure from open-ring isomers to closed-ring isomers. Therefore these cyanine-based compounds could be applied not only in photochromic materials, but also they could be used as fluorescence switches. Accordingly, one of these compounds was successfully used in the biological imaging of living cells. These results suggest that cyanine-based dithienylethenes may be used as photoswitchable bio-materials in the future.