Background <p><i>Deschampsia antarctica</i>, one of only two native vascular plants in Antarctica, provides a model for studying plant adaptation in extreme environments. Despite its ecological significance, genetic data for this species remain limited. Understanding its genetic variability is essential for assessing its adaptive potential amid rapid climate change. This study investigated the genetic diversity and population structure of <i>D. antarctica</i> from seven locations across the Antarctic Peninsula using Inter-Primer Binding Site (iPBS) retrotransposon markers.</p> Methods and results <p>Forty-five iPBS primers generated 1,400 scorable bands, 98.9% of which were polymorphic, indicating the high discriminatory capacity of the markers. Cluster analyses (UPGMA and PCoA) identified two major genetic lineages: Livingston–Ridge and King George–Ardley–Galindez–Lagotellerie populations, with pairwise similarities ranging from 0.994 to 0.999. AMOVA showed that 96% of total genetic variation occured within populations, reflecting substantial intra-population diversity and minimal inter-populations. The low inter-population differentiation likely reflects recent post-glacial expansion (~ 10,000 years ago), clonal propagation, and polyploid buffering, which maintain within-population variation while limiting divergence.</p> Conclusion <p>These results exceed previous diversity estimates, showing that <i>D. antarctica</i> maintains extensive genetic variation despite environmental isolation. The study demonstrates the effectiveness of iPBS markers in resolving fine-scale genetic patterns and provides new insights into the evolutionary dynamics, population structure, and conservation strategies for Antarctic flora under changing climatic conditions.</p>