•Peroxynitrite is irreplaceable physiological activator and signaling molecule in living organisms.•A review of oxidized peroxynitrite imaging fluorescent probes based on reactive recognition sites and its imaging studies in biological systems.•Systematic conclusion and classification of reaction recognition sites for peroxynitrite fluorescent molecular probes.•This review can provide an empirical reference for the design and synthesis of subsequent ONOO– fluorescent probes. Peroxynitrite, one of the most active reactive oxygen (ROS) and reactive nitrogen (RON) species, has been of wide interest because of its high oxidizing and nitrifying properties. As a vital physiological activator and signaling molecule, peroxynitrite (ONOO–) excess can damage proteins, nucleic acids, and amino acids in cells, thus causing inflammation and other serious diseases in living organisms. Fluorescence sensing and fluorescence imaging can label and track a wide range of biological activities and living molecules with excellent temporal and spatial resolution. As a result, many small molecule fluorescent probes have been developed for the detection and treatment of peroxynitrite. However, this interesting and cutting-edge topic has not been systematically summarized so far. Therefore, this review highlights the design strategies, reaction mechanisms, and imaging applications of organic fluorescent probes used for peroxynitrite detection in recent years. In particular, a detailed summary and description of the recognition sites for peroxynitrite (ONOO–) are provided, which can facilitate fresh ideas and inspiration for future research efforts. More meaningfully, we hope that the future developments of fluorescent probes for detecting ONOO– can overcome the current problems, such as limited water solubility, high biological toxicity, etc., and create a superior and safer fluorescent sensing technology.