Population living at high altitudes may offer a unique demographic history to study. Ladakh is one such region where the human population live at an average altitude of 12500 feet. We have genotyped 21 autosomal STR markers among 122 samples from the Central Ladakh region. We first showed the high forensic potential of forensic markers among these isolated populations based on the forensic parameters. We also evaluated the genetic affinity of these populations by employing various statistical methods. Statistical tests based on STR genotype data showed no significant departure from Hardy-Weinberg Equilibrium (HWE) except loci D10S1248 and D2S441. The overall match probability, combined power of exclusion and combined power of discrimination for these loci were 7.660 x 10-24, 0.999999968762 and 0.99999999999, respectively. The locus SE33 was found to be the most efficient forensic loci. Furthermore, Fst based analysis suggested a closer affinity of the studied group with the Nepal, Bhutan and Tibetan populations. The Neighbour-Joining tree revealed the Central Ladakh group as drifted branch comprised mainly of the Nepal and Tibet cluster. This study supports the notion that the genetic landscape of Ladakh is similar to low-land India, where gene follows geography. The structure analysis suggested the mixed ancestry of the Central Ladakh population primarily associated with South Asia, East Eurasia and West Eurasia.