There has been a debate over the effect of the fluctuating climatic conditions on ecosystems worldwide. Nevertheless the fact that frost requirement for a particular growth/development pattern in the life cycle of an organism will always hold a prerequisite. Within the Rhododendron genera, Rhododendron arboreum dominates the warm temperate Himalayan zones and has been of commercial, and landscaping values besides being a keystone species and a warehouse of bioactive secondary metabolites. The present scenario of global warming exaggerated by anthropogenic activities could deteriorate the existence of species in near future. As a non-model species with relatively meagre genomic data available, transcriptome can offer insight into the active gene networking and can be utilized as a high-throughput marker database. The paired-end tissue-specific raw data was pre-processed and subjected to Trinity-based de novo assembly. From 71961 annotated transcripts, 100 were selected for primer designing. Till date of the 35 primers characterized that comprised only of tri- and di-repeats, 22 showed 100% polymorphism on 30 genotypes belonging to three populations of the Himalayan states. The approximate length of the amplified fragments varied from 140-300 bp with allele-number ranging from 2-9, with observed and expected heterozygosity averaging to 0.367and 0.593, respectively. The SSRs designed can be employed for population structure and other genetic studies that in turn can be projected to imply conservation strategies for a threatened species.
