Provided herein are improved fluorogenic compounds and probes that can be used as reagents for measuring, detecting and/or screening peroxynitrite. The fluorogenic compounds of the invention can produce fluorescence colors, such as green, yellow, red, or far-red. Also provided herein are fluorogenic compounds for selectively staining peroxynitrite in the mitochondria of living cells. Provided also herein are methods that can be used to measure, directly or indirectly, the presence and/or amount of peroxynitrite in chemical samples and biological samples such as cells and tissues in living organisms. Also provided are high-throughput screening methods for detecting or screening peroxynitrite or compounds that can increase or decrease the level of peroxynitrite in chemical and biological samples.