Mercury (Hg) is one of the major toxic heavy metals because it bioaccumulates and biomagnifies in animal and human bodies via the food chain. To eliminate heavy metal contamination, plants are being used as removal agents of pollutants/toxic chemicals from the environment. The present study was mainly focused on elucidating the potential phytotoxic effects of Hg heavy metal ion exposure on Sesbania grandiflora seedlings. Growth of seedlings was significantly affected (56 %) at 60 mg L−1 Hg concentration. The level of chlorophyll pigment contents was increased in Hg-treated plants compared to the control. Malondialdehyde content and antioxidative enzyme activities were found to be significantly increased by increasing the concentration of Hg exposure up to 40 mg L−1 while slightly decreased at higher doses. The DNA alterations appearing in the random amplified polymorphic DNA (RAPD) profiles of leaf and root tissues following Hg heavy metal exposure included the disappearance of normal DNA bands and the appearance of new bands compared to the untreated controls. This result strongly indicated that genomic template stability was significantly affected by Hg-induced stress in S. grandiflora seedlings. It is concluded that DNA polymorphisms detected by RAPD fingerprinting analysis could be used as potential molecular markers for the evaluation of Hg heavy metal ion-induced genotoxic effects in other plant species.