Isozyme can provide effective information on the genetic variations at inter- and intra- populations level. The results reported in this paper concern the genetic variations in Rubia cordifolia L., which is a dye yielding plant. Seeds were collected from five different climatic conditions. Polyacrylamide gel electrophoresis study of eleven enzymes revealed 40 putative alleles. Among the 40 putative alleles, 21 were found in all populations. Allelic frequency and polymorphic loci were determined for each population and the data were further subjected to Cluster analysis. The results revealed greater genetic variations at lower altitude populations than at higher. : Alleles, allelic frequency, Isozymes, R. cordifolia, polymorphic loci, dendrogram, genetic variation. I. NTRODUCTION Rubia cordifolia L., commonly known as Indian madder or Bengal madder, belongs to the family Rubiaceae. It is a tropical wild plant, growing in hills above 800 meters as thickets. It is a rugose vine with quadrate stem, profusely branched and grows up to 10 meters height. The flowers in dichasial cymes are white to greenish color with peak flowering during November to January. Fruit is a drupe. Indian madder is a source of natural madder dye, which is obtained from roots. The coloring matter present is a mixture of purpurine and munjistin [1]. Genetic diversity is an ubiquitous property of all species in nature. The distribution and organization of genetic variation within populations of a species are the consequences of its evolution. As an important tool to assess genetic diversity, isozyme variation in many plants and their wild relatives has been extensively surveyed in relation to their geographic distribution [2-6]. Many researchers have also studied the genetic variability at inter- and intra- population levels for the purpose of gene pool conservation [7, 8]. In this paper, we have studied genetic diversity in R. cordifolia using isozyme markers in order to exploit the results for future improvement of the taxon for better dye content.