Cyanine dyes, as used in super‐resolution fluorescence microscopy, undergo light‐induced “blinking”, enabling localization of fluorophores with spatial resolution beyond the optical diffraction limit. Despite a plethora of studies, the molecular origins of this blinking are not well understood. Here, we examine the photophysical properties of a bio‐conjugate cyanine dye (AF‐647), used extensively in dSTORM imaging. In the absence of a potent sacrificial reductant, light‐induced electron transfer and intermediates formed via the metastable, triplet excited state are considered unlikely to play a significant role in the blinking events. Instead, it is found that, under conditions appropriate to dSTORM microscopy, AF‐647 undergoes reversible photo‐induced isomerization to at least two long‐lived dark species. These photo‐isomers are characterized spectroscopically and their interconversion probed by computational means. The first‐formed isomer is light sensitive and transforms to a longer‐lived species in modest yield that could be involved in dSTORM related blinking. Permanent photobleaching of AF‐647 occurs with very low quantum yield and is partially suppressed by the anaerobic redox buffer.