Himalayan region is one of the important hotspot, having Rhododendron arboreum as major species. Anthropogenic activities and unsustainable use of the plant for its fruits, flower and wood by local people has raised questions about the sustainability of the species. In order to answer these questions, it is important to first know the genetic structure of the population. This study is focused on the characterization of the G-SSR markers for Rhododendrons and to study the population genetic structure. A set of 38 primers out of 41 are characterized on three population of Rhododendron arboreum, a total of 30 individuals. Allele number at different loci came to be in range of 2 to 14 with an average of 5.2 alleles per locus. Level of heterozygosity observed was high which varies from 0.422 to 0.917 (He) and 0.167 to 0.933 (Ho) with a polymorphic information content 0.104 to 0.811. Out of 38, about 19 loci deviated from the Hardy Weinberg Equilibrium. Genetic diversity was high in these populations with an average gene flow of 5.436. Based on the information from the loci, there was no observed linkage disequilibrium and bottleneck effect. Software DARwin and STRUCTURE, irrespective of geographical location, revels the presence of two original populations with admixed genetic stock. These studied loci will help in the further genetic mapping of the genes and genotyping studies in Rhododendron arboreum.