A random amplified polymorphic DNA (RAPD) analysis was made to determine the genetic variation between the five populations of the medicinal shrub, Acacia caesia var. caesia in an environmental gradient. Of the nine random primers tested, one primer, UBC-807 showing polymorphism was used in RAPD analysis. The primer produced 12 scorable DNA fragments in the populations studied, which showed the existence of genetic variation between populations. Adendrogram was constructed based on Jaccard’s coefficient to determine the degree of genetic relationship among the five populations and analysed. It showed that the genetic similarity amongthe populations varied from 55 to 89 %. Further, the genetic polymorphism in the population in a very arid habitat at Chennimalai was higher (70%) than that of other populations, which indicates the plasticity of the genome in a water-stressed environment. Observation of morphological features shows that the population in a very arid habitat had decreased vegetative growth withincreased reproductive attributes.