Western Himalayan yew (Taxus contorta Griffith, synonym T. fuana Nan Li & R.R. Mill), one of the highly prized tree species for its anticancer properties is experiencing severe reduction in populations across its range in Pakistan. We examined a chloroplast DNA region (trnL-F) and ten nuclear microsatellite loci variations among seven populations to investigate the levels of genetic diversity and demographical history of T. contorta in Pakistan. Low haplotype diversity (HT = 0.182), moderate level of microsatellite diversity (HE = 0.526 ± 0.034), significant population differentiation (FST = 0.106) and high level of inbreeding (FIS = 0.222-0.418) was found in T. contorta compared with its congeners. Results of mismatch distribution analysis, neutrality tests and data on glacial chronologies of western Himalaya indicated that demographic expansion of T. contorta in Pakistan predates extensive glaciations that occurred during late Pleistocene (140.06 thousand years ago (kya), and the spatial expansion most likely happened very recently in the Holocene (6.71 kya). An unprecedented level of habitat disturbances since past few decades coupled with the severe historic climate may have played an important role on an extant population structure of T. contorta. We have discussed a range of sustainable management measures for the ecological restoration of remnant populations as well as to exploit high economic benefits that can be obtained from this species.