Many environmental contaminants have been reported to disturb the pro-oxidant or antioxidant balance of the cells by inducing oxidative stress. Oxidative stress mediated by the HgCl₂ induces DNA, protein and lipid oxidation resulted in necrosis or apoptosis, or both. Currently flavonoids are being emerging topic and reported to have antiviral, anti-inflammatory, anti- tumor and antioxidant activities. Morin is one of the flavonoid protects the cells from oxygen free radical damage and scavenges the free radicals and metals and also heals the injured cells commercially. Morin hydrate is sparingly soluble in water. Hence, the water soluble morin -5′- sulfonic acid sodium salt (NaMSA) was selected and synthesized. Aim of the present study was to analyze the effect of morin-5′-sulfonic acid sodium salt on the expression of apoptosis related proteins caspase 3, Bax and Bcl 2 due to the mercury induced oxidative stress in albino rats.. The experimental rats were exposed to sub lethal concentration of mercuric chloride (1.25mg/kg) and the ameliorating effect of NaMSA was studied by using apoptotic protein markers Bax and caspase-3 and Bcl-2. The obtained results were analyzed using one way analysis of variance by the Duncan’s Multiple comparison test to determine the level of significance (p) and p<0.05 was considered as statistically significant. Administration of mercuric chloride (1.25mg/kg) in the experimental rats increased the expression of Bax and caspase-3 and a decreased expression was noted in the Bcl-2 level compared with control bands significantly (p<0.05). On the other hand NaMSA (50mg/kg) and HgCl₂ (1.25mg/kg) simultaneous administration did not bring any change in the protein expression of Bax, Caspase-3 and Bcl-2 levels compared with control rats. Hence, the membrane damage was protected, stopped the cell death and apoptosis. This could be due to the morin-5′-sulfonic acid sodium salt effective chelation action on the HgCl₂ generated free radicals.