As subalpine ecosystems are suffering series of changes caused by global climate change, many subalpine tree species are threatened and gradually becoming locally extinct. A. mariesii, recognised as the foundation species in a subalpine ecosystem which receives extraordinarily heavy winter snowfall in central Japan, is maintaining its populations by showing highly plastic morphologies across different sites. Considering the high morphological variations of A. mariesii that revealed by earlier data, this study aims to unearth the genetic responses of A. mariesii populations to heterogeneous environmental conditions at the local scale. Six populations from both heavily and less snowy sites were sampled using 6 microsatellite markers. We observed high genetic diversity in A. mariesii populations. Analysis of Molecular Variance suggested that most genetic variation was partitioned within populations. No Isolation By Distance patterns were detected for all pairwise comparisons between populations, and gene flow among A. mariesii populations was also likely to be restricted due to asynchronous snowmelt timing across the sites.