The effect of equimolar concentrations of Hg 2+ and Cd 2+ on the whole cell absorption spectra, absorption spectra of the extracted phycocyanin (PC) and fluorescence emission spectra of phycobilisomes (PBS) was investigated in the cells of Anabaena flos-aquae. The PC component of the PBS was found to be extremely sensitive to the Hg 2+ rather than the Cd 2+ ions. Further, the results showed that Hg 2+ and Cd 2+ induced decrease in the rate of Hill activity (H20 -DCPIP) was partially restored by the electron donor NH2OH, not by the diphenyl carbazide. Similarly, chlorophyll a fluorescence emission in the presence of metals showed that addition of NH2OH could effectively reverse the metal induced alterations in the fluorescence emission intensity. These results, together, suggested that Hg 2+ and Cd z+ caused damage to the photosystems (PS) II reaction center. However, a relatively higher stimulation of the chlorophyll a emission at 695 nm with a red shift of 4.0 nm in the presence of Hg 2+ , and Cd 2+ induced preferential decrease in the emission intensity at 676 nm as compared with the peak at 695 nm were indicative of the differential action of Hg 2+ and Cd z+ on the PS II.