Peroxynitrite (ONOO-) is known to inactivate important cellular targets and also mediate oxidative damage in DNA, The present study has demonstrated that phycocyanin, a biliprotein from spirulina platensis and its chromophore, phycocyanobilin (PCB), efficiently scavenge ONOO-, a potent physiological inorganic toxin, Scavenging of ONOO- by phycocyanin and PCB was established by studying their interaction with ONOO- and quantified by using competition kinetics of pyrogallol red bleaching assay. The relative antioxidant ratio and IC50 value clearly indicate that phycocyanin is a more efficient ONOO- scavenger than PCB. The present study has also shown that PCB significantly inhibits the ONOO--mediated single-strand breaks in supercoiled plasmid DNA in a dose-dependent manner with an IC50 value of 2.9 +/- 0.6 muM. These results suggest that phycocyanin, has the ability to inhibit the ONOO--mediated deleterious biological effects and hence has the potential to be used as a therapeutic agent.