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Scots pine (Pinus sylvestris L.) spans most of Eurasia, yet southern and mountainous populations may retain distinctive genetic components shaped by long-term isolation and complex postglacial dynamics. We genotyped 186 trees from four Scots pine stands in Armenia (AM1-AM4) and reference stands from Germany, Russia and Montenegro with the PiSy50k SNP array and integrated these data with published European array datasets from Finland, Poland and the Baltic region. After quality checks and conservative SNP filtering, 627 individuals from 47 populations and 3659 SNP loci were retained. Within-population diversity was generally high; Armenian stands AM2–AM4 were among the most diverse, whereas AM1 showed reduced diversity and the highest differentiation relative to the remainder of the dataset (FST vs. rest = 0.0047). Direct pairwise FST and hierarchical AMOVA confirmed pronounced heterogeneity among Armenian stands, with AM1 the most differentiated stand, AM2 and AM4 closest to the broader Eurasian background, and AM3 intermediate. Principal component analysis (PC1 = 1.42%, PC2 = 0.76%) again separated AM1 strongly from all non-Armenian samples, while AM2 overlapped with the central/eastern European cluster and AM3 and AM4 combined continental-like and AM1-like individuals. Structure-like inference with LEA/sNMF showed a broad cross-entropy plateau from approximately K = 4 to K = 6; we therefore use K = 5 as a practical summary, which highlighted a dominant AM1-associated ancestry component and variable continental admixture in AM2–AM4. KING kinship estimates provided little evidence for within-stand family clustering in Armenian stands; no second-degree-or-closer pairs were observed in AM1–AM4. Together, the results reveal pronounced heterogeneity among Armenian Scots pine stands and identify AM1 as a highly differentiated but unresolved genomic component, providing a genomic baseline to support conservation planning, provenance evaluation and the management of forest reproductive material in the Lesser Caucasus.