Abstract Polymethine cyanine dyes have witnessed significant advancements in bioimaging and phototherapy due to their optical properties and ease of modification. This review categorizes and introduces typical synthesis of Cy3, Cy5, Cy7 and longer polymethine cyanine dyes, and highlights organic‐specific in‐cell synthesis of cyanines via the newly‐established pseudo‐trimerization method using a single exogenous precursor activatable by visible light, free radicals or reactive oxygen species. Further discussions delve into the functionalization strategies and structure‐activity relationships of cyanine dyes, and summarizes bioapplications of cyanines in fluorescence imaging, phototherapy and multimodal assisted diagnosis and treatments, aiming to unlock the full potential of cyanine dyes in scientific research and clinical translation.