Population genetic structure can be defined as the temporal distribution of gene and genotype frequencies of a population. In support of the isolation by distance model of Wright (1943) simulations shows that under restricted gene flow and selective neutrality, the population as a whole develops a patchy distribution of genotypes. In this study 3 populations of Picrorhiza kurrooa were sampled from habitats that may have different historical geologic processes. The region under study is a physiographically complex mountainous territory, so it represents an excellent model system to study the effect of mountain ranges as barriers to interpopulational gene flow. One population was located in the greater Himalayas (Ladakh range) and lies to the north of the main Himalaya the other 2 populations were collected from middle Himalayans (Sonamarg and Gurez) to the south of the Himalayan terrain. Spatial analysis of population genetic structure by RAPD provides relevant molecular genetic information about fragmentation patterns and landscape genetics that shape population genetic structure and adaptive genetic variation in natural populations of Picrorhiza kurrooa.