The steep and complex topography in high-elevation mountains usually generates heterogeneous habitats, where reproductive isolation in spatially discrete populations, such as unsynchronized flowering, likely occurs. Therefore, genetically differentiated populations in some cases can be expected. Patterns of genetic variation and directions of gene flow among discrete populations could hold crucial information for a better understanding of population genetic structures in heterogeneous habitats. In this study, we examined the local-scale genetic structure and gene flow patterns among Abies mariesii populations in a heterogeneously snowy subalpine ecosystem. We found that A. mariesii populations, though spatially discrete and undergoing strong habitat heterogeneity, are less likely to be genetically differentiated. Gene flow was biased toward the moorlands, and compared to the forest populations, the genetic diversity in the moorland populations was found to be significantly higher, suggesting that the moorlands could serve as sinks of genetic diversity for A. mariesii. Finally, we quantified the morphological variation of A. mariesii and discovered that being able to adjust tree morphology in contrasting eco-habitats may strengthen the competitiveness of A. mariesii. This may also make a tangible contribution to the maintenance of populations in contrasting habitats.