Cissus quadrangularis is an ancient medicinal plant native to the hotter parts of Srilanka and India. Cissus quadrangularis has been used by common folk in India for promoting the fracture healing process. Cissus quadrangularis belongs to the family Vitaceae and genus Cissus Linn, used for the treatment of antihelmintic, analgesic in eye and ear diseases, and in the treatment of irregular menstruation, asthma. The present paper deals with the molecular assay of Cissus quadrangularis L. The present investigation deals with before and after inoculation of pathogen E-coli into Cissus quadrangularis at different concentration of inoculums (0.5 ml, 1 ml and 1.5ml). After 24, 48 and 72 hours incubation the plant parts are cut, dried and powdered. The powdered samples taken for molecular assay. The molecular characterization of DNA over the period of incubation shows that the number of bands increases with time in each of the species and are more when compared to control readings. The frequency profile of RAPD bands were studied with respect to UPGMA band analysis using alpha imager software. Comparative study of the molecular assay of DNA profile of the control and the treated one was done to locate the specific site of DNA that could be targeted for Drug designing in future.