The genomic DNA polymorphism variation of Stevia rebaudiana Bertoni was investigated by RAPD-PCR analysis. For initial PCR screening, about hundred Oligo-nucleotide primers were used to amplify the genomic DNA from three accessions of Stevia rebaudiana (S1 to S5). A total of a primer were finally selected to generated RAPD fingerprints that revealed III bands, which 88 bands (80%) were found to be polymorphic bands. Five accessions were clustered in to two major groups in the dendrogram. The present results suggested that there was strong correlation between the variables in DNA polymorphism data. The present study concluded that the results of the genetic diversity could be used to select best accessions for planting and conservation of the Stevia rebaudiana pharmaceutical applications.