Biotic and abiotic stresses exert a significant influence on the growth and reproduction of plants. Temperature, pH, light, water, salinity and various chemical pollutants are the important abiotic stresses which directly affect the survival, growth, reproduction and geographical distribution of all plants. The present study explains the heavy metal stress tolerance potential of two halophytes viz. Avicennia officinalis L. and Rhizophora mucronata Poir. in Lam. Physiological and biochemical assays were conducted on the plant and soil samples collected from the polluted areas of Kodungallur, Kerala. Results of the study indicated that A. officinalis L. shows better stress tolerance by accumulating low amount of proline and MDA and high amount of photosynthetic pigments which in turn allowed their better establishment in the polluted habitat. The phytoremediation potential was analysed by quantifying the heavy metals (Cr, Cd and Pb) from plant parts - root and leaf and also from the soil samples collected from their habitat. The assay indicated that the phytoremediation potential is higher in Avicennia officinalis L. and it was confirmed by the higher uptake of heavy metals by the plant when compared to that of the Rhizophora mucronata Poir. in Lam. We recommends the use of halophyte Avicennia officinalis L. for the phytoremediation of polluted saline areas.