The genetic landscape of yerba mate (Ilex paraguariensis) remains poorly understood across its core distribution range -represented in this study by Misiones, Argentina- despite the species’ profound cultural and economic importance. We aimed to characterize the genetic diversity, population structure, and centre‑periphery dynamics of wild I. paraguariensis. To this end, we compared an Atlantic Forest remnant at Campo Anexo Manuel Belgrano (CAMB) in Misiones, Argentina, with Uruguayan populations. For this comparison, we used genetic data from 148 CAMB individuals (12 populations) and 56 plants from Uruguay (6 populations). Allele sizes were determined by automated fragment analysis. Preliminary analyses suggested that CAMB individuals function as a metapopulation. The present data indicates that CAMB exhibited high genetic diversity (H̅ₒ = 0.481, H̅ₑ = 0.568; total alleles = 48; private alleles = 22), low but significant differentiation (FST = 0.037), and weak isolation‑by‑distance (IBD: r = 0.355; p = 0.027). Unsupervised DAPC clustering revealed shallow genetic structure and admixture across Argentinian samples. Uruguayan populations displayed marked genetic erosion indicated by reduced allelic diversity (total alleles = 33), lower heterozygosis (H̅ₒ = 0.264), high differentiation (FST = 0.300), and limited gene flow (Nm = 0.816), consistent with divergence expected at range margins. Hierarchical AMOVA attributed 16.1% of total genetic variation to differentiation between core and peripheral regions (FRT = 0.161), with significant IBD across the entire sampling range (r = 0.424; p < 0.001). These findings demonstrate that CAMB forest remnants constitute a high‑diversity genetic reservoir, reliant on interconnected subpopulations for full allelic representation, whereas Uruguayan peripheral populations appear drift-driven and isolated. Management must thus combine the in-situ protection of this core reservoir with the ex-situ banking of rare and private alleles across both regions.