DNA fingerprinting has been widely applied to examine the genetic variation for the purpose of biological conservation. DNA microsatellites with short sequence repeats provide high variability and high resolution in assessing population genetic structure. In this study, microsatellite polymorphisms and genetic structure of Juniperus squamata were examined. Genetic diversity within populations of J. squamata were high. In J.squamata, it posses high levels of population differentiation mediated with the limit of gene flow and adaptation of local environmental conditions. However, 87.81% of the genetic variation is harboured within populations. It may be sufficient to maintain a few populations across the whole distribution range to ensure that the genetic diversity is represented.