The genus Rhododendron belongs to the family Ericaceae. It is an ecologically and medicinally newlineimportant species of the Himalayan Region. In present study SSR and AFLP markers with newlineRemote Sensing and GIS data are used for monitoring the impact of temperature and altitude newlineon the spatial distribution and dispersal of species to understand its structure, diversity and newlinedifferentiation. 27 SSR primers were used for the genotyping of 24 populations comprised of newline260 samples. The average Fst and Nm found to be 0.237 and 1.095 respectively, which shows newlinethe differentiation in the populations. The temperature impacts 14% and altitude 30%, the gene newlineflow for population differentiation. The temperature and altitude with some physical barriers in newlinethe form of mountain ranges were found, which creates temporal isolation in the distribution of newlineR.arboreum. Eight primer combinations of AFLP markers were also used for the genotyping of newlinethe same samples. The average value of (Gst), was found to be 0.15 and Nm values was found newlineto be 2.798. The Himalayan region has undergone significant changes due to various newlineanthropogenic activities, which reduced the species spatial distribution to 1.63% in 2017 as newlinecompared to 2002 and water bodies occupied as 17.70 percent with the increment of 1.79% newlinedue to shrinkage of glaciers and global warming. In physico-chemical analysis of soil samples, newlinethe mean pH, Mean Electrical Conductivity, Water Holding Capacity (WHC) values across all newlinethe soil samples shows acidic, non-saline nature of soil i.e. 5.5, 1.219dS/m and 43.12% newlinerespectively. The elevated levels of heavy metals like Fe, Hg, and Mn from their permissible newlinelimits indicate the alarming signal of soil pollution in the Himalayan region. The present study newlineinvestigates the main reasons behind the genetic differentiation, shaping of gene pool and newlinechanging patterns of dispersal of R. arboreum in Indian Himalayan region and provides newlinesuggestions to plan new conservation strategies.