The Union Territory of Jammu and Kashmir has always been a point of contention among India, Pakistan, and China for various reasons. This region has great significance historically due to its geography and ethnic diversity. However, a comprehensive genetic study providing the genetic landscape of Jammu and Kashmir was lacking until now. In this study, we analysed 21 hyper-variable autosomal STR loci of 694 individuals from Jammu and Kashmir and compared them with neighbouring populations to explore the genetic implications of demographic dynamics that have taken place in this region. Our findings suggest that the population of Jammu and Kashmir is a genetic mixture of two major clines, northern and southern, that correspond with the variation in geography, linguistics, and demography of the region. Broadly, the gene flow into the southern cline appears to be in historical times perhaps as a result of the spread of Gurjars, Dogri language and invasions of Mongols. However, the arrival of ancient nomadic tribes into this region may belong to the time depth of the arrival of pastoralist communities in this region. As a future perspective, a comprehensive study including samples from individual tribes will provide fine-scale structure of the gene pool of Jammu and Kashmir.